| Type |
Details |
Score |
| Protein Domain |
| Name: |
Sirohaem synthase |
| Type: |
Family |
| Description: |
Sirohaem synthase (CysG), a multifunctional enzyme of the sirohaem and cobalamin (vitamin B12) biosynthesis pathways, represents a fusion between uroporphyrin-III C-methyltransferase (SUMT) and precorrin-2 oxidase/chelatase. Therefore, in some bacteria, all four reactions of sirohaem biosynthesis are catalysed by one multifunctional enzyme, sirohaem synthase [
].Sirohaem and cobalamin are related macrocyclic structures derived from uroporphyrinogen III by C-methylation of the tetrapyrrole framework. All biologically important modified tetrapyrroles (including also haem and chlorophyll) share a common biosynthetic pathway up to the synthesis of the first macrocyclic intermediate, uroporphyrinogen III [
]. Then, SUMT (corresponding to the C-terminal (CysGA) domain of CysG ([]) catalyses C-methylation of uroporphyrinogen III (). It transfers two methyl groups from S-adenosyl-L-methionine to the C-2 and C-7 atoms of uroporphyrinogen III to yield precorrin-2 via the intermediate formation of precorrin-1. SUMT is the first enzyme committed to the biosynthesis of either sirohaem or cobalamin rather than haem, and precorrin-2 is the last common intermediate in the biosynthesis of corrinoids such as cobalamin, sirohaem and coenzyme F430 [
]. SUMT belongs to the domain superfamily of tetrapyrrole (corrin/porphyrin) methylases (), which includes methylases that use S-AdoMet in the methylation of diverse substrates.
In sirohaem biosynthesis, the next two steps are beta-NAD(
+)-dependent dehydrogenation of precorrin-2 to generate sirohydrochlorin followed by ferrochelation to yield sirohaem [
,
]. Both of these steps are performed by precorrin-2 oxidase/ferrochelatase. In sirohaem synthase CysG, it corresponds to the N-terminal (CysGB) domain [,
]. Ferrochelation can also be performed by CbiK () [
] or by SirB [] or CbiX [].In the anaerobic cobalamin biosynthesis (e.g., in Salmonella typhimurium), a cobaltochelatase produces cobalt-precorrin-2. This cobaltochelation can be performed by CbiK [
] or by CbiX [,
], but also by CysGB homologues [], even though this is not their primary function []. Therefore, CysGB can essentially duplicate the function of an unrelated chelatase, CbiK [,
]. Note that in the aerobic cobalamin biosynthesis, cobalt insertion occurs in a later, different step (see ).
Precorrin-2 oxidase/chelatases are not similar in sequence or structural fold to any other known chelatases or oxidases [
,
]. Analysis of mutant proteins suggests that both catalytic activities share a single active site cleft formed between the N-terminal NAD-binding subdomain and the central subdomain []. Therefore, they can be considered as the third class of cobalt chelatases, in addition to class I (ATP-dependent, aerobic pathway ) and class II (ATP-independent, anaerobic pathway
) [
,
]. As with the class II chelatases, they do not require ATP for activity. However, they are not structurally similar to class II chelatases, and it is likely that they have arisen by the acquisition of a chelatase function within a dehydrogenase catalytic framework [,
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Aminopeptidase N-type |
| Type: |
Family |
| Description: |
This M1 peptidase family includes eukaryotic and bacterial members: aminopeptidase N (APN; MEROPS identifier M01.001), aminopeptidase Q (APQ, laeverin; MEROPS identifier M01.026) [
,
], endoplasmic reticulum aminopeptidase 1 (ERAP1; MEROPS identifier M01.018) [] as well as tricorn interacting factor F3 (MEROPS identifier M01.021).Aminopeptidase N (APN; CD13; Alanyl aminopeptidase;
), a type II integral membrane protease, consists of a small N-terminal cytoplasmic domain, a single transmembrane domain, and a large extracellular ectodomain that contains the active site. It preferentially cleaves neutral amino acids from the N terminus of oligopeptides and is present in a variety of human tissues and cell types (leukocyte, fibroblast, endothelial and epithelial cells). APN expression is dysregulated in inflammatory diseases such as chronic pain, rheumatoid arthritis, multiple sclerosis, systemic sclerosis, systemic lupus erythematosus, polymyositis/dermatomyosytis and pulmonary sarcoidosis, and is enhanced in tumor cells such as melanoma, renal, prostate, pancreas, colon, gastric and thyroid cancers. It is considered a marker of differentiation since it is predominantly expressed on stem cells and on cells of the granulocytic and monocytic lineages at distinct stages of differentiation. Thus, APN inhibition may lead to the development of anti-cancer and anti-inflammatory drugs [
,
].ERAP1 also known as endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP), adipocyte derived leucine aminopeptidase (A-LAP) or aminopeptidase regulating tumor necrosis factor receptor I (THFRI) shedding (ARTS-1), associates with the closely related ER aminopeptidase ERAP2 (MEROPS identifier M01.024), for the final trimming of peptides within the ER for presentation by MHC class I molecules. ERAP1 is associated with ankylosing spondylitis (AS), an inflammatory arthritis that predominantly affects the spine. ERAP1 also aids in the shedding of membrane-bound cytokine receptors [
].The tricorn interacting factor F3, together with factors F1 and F2, degrades the tricorn protease products, producing free amino acids, thus completing the proteasomal degradation pathway. F3 is homologous to F2, but not F1, and shows a strong preference for glutamate in the P1' position [
].APQ, also known as laeverin, is specifically expressed in human embryo-derived extravillous trophoblasts (EVTs) that invade the uterus during early placentation [
]. It cleaves the N-terminal amino acid of various peptides such as angiotensin III, endokinin C, and kisspeptin-10, all expressed in the placenta in large quantities.APN is a receptor for coronaviruses, although the virus receptor interaction site seems to be distinct from the enzymatic site and aminopeptidase activity is not necessary for viral infection [
]. Insect APNs (MEROPS identifiers M01.013 and M01.030) are also putative Cry toxin receptors. Cry1 proteins are pore-forming toxins that bind to the midgut epithelial cell membrane of susceptible insect larvae, causing extensive damage. Several different toxins, including Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to bind to APNs; however, a direct role of APN in cytotoxicity has been yet to be firmly established []. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
RNA-directed RNA polymerase, catalytic domain |
| Type: |
Domain |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [
].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents the catalytic domain of the RNA-directed RNA polymerase from all positive-strand RNA eukaryotic viruses with no DNA stage. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Carbamoyl-phosphate synthase, large subunit |
| Type: |
Family |
| Description: |
Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (
) or ammonia (
), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [
,
]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase () (ACC), propionyl-CoA carboxylase (
) (PCCase), pyruvate carboxylase (
) (PC) and urea carboxylase (
).
Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain [
]. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein [
]. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents glutamine-dependent CPSase (
) from prokaryotes and eukaryotes (CPSase II).
|
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Carbamoyl-phosphate synthase large subunit, CPSase domain |
| Type: |
Domain |
| Description: |
Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (
) or ammonia (
), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [
,
]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase () (ACC), propionyl-CoA carboxylase (
) (PCCase), pyruvate carboxylase (
) (PC) and urea carboxylase (
).
Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain [
]. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein [
]. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the CPSase domain of the large subunit of carbamoyl phosphate synthase. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
RNA-directed RNA polymerase, apple chlorotic leaf spot virus |
| Type: |
Domain |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
P-type ATPase, B chain, subfamily IA |
| Type: |
Family |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.P-ATPases (also known as E1-E2 ATPases) ([intenz:3.6.3.-]) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H+, Na
+, K
+, Mg
2+, Ca
2+, Ag
+and Ag
2+, Zn
2+, Co
2+, Pb
2+, Ni
2+, Cd
2+, Cu
+and Cu
2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.
These sequences describe the P-type ATPase subunit of the complex responsible for translocating potassium ions across biological membranes in microbes. In Escherichia coli and other species, this complex consists of the proteins KdpA, KdpB, KdpC and KdpF. KdpB is the ATPase subunit, while KdpA is the potassium-ion translocating subunit [
]. The function of KdpC is unclear, although it has been suggested to couple the ATPase subunit to the ion-translocating subunit [], while KdpF serves to stabilise the complex []. The potassium P-type ATPases have been characterised as Type IA based on a phylogenetic analysis which places this clade closest to the heavy-metal translocating ATPases (Type IB) []. Others place this clade closer to the Na+/K+ antiporter type (Type IIC) based on physical characteristics []. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Viral RNA-directed RNA polymerase, 4-helical domain |
| Type: |
Homologous_superfamily |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This superfamily represents a subdomain of the viral RNA-directed RNA polymerase. Its structure consists of 4 α-helices. |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2636
|
| Description: |
aspartate--tRNA ligase, mitochondrial-like isoform X1 [Glycine max]; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0016874 (ligase activity) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
4343
|
| Description: |
coatomer subunit alpha-2-like isoform X2 [Glycine max]; IPR006692 (Coatomer, WD associated region), IPR015943 (WD40/YVTN repeat-like-containing domain), IPR020472 (G-protein beta WD-40 repeat); GO:0005198 (structural molecule activity), GO:0005515 (protein binding), GO:0006886 (intracellular protein transport), GO:0016192 (vesicle-mediated transport), GO:0030117 (membrane coat) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2623
|
| Description: |
elongation factor Tu GTP-binding domain protein; IPR004540 (Translation elongation factor EFG/EF2), IPR005225 (Small GTP-binding protein domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003746 (translation elongation factor activity), GO:0003924 (GTPase activity), GO:0005525 (GTP binding), GO:0005622 (intracellular), GO:0006414 (translational elongation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2423
|
| Description: |
high mobility group B protein 15-like isoform X7 [Glycine max]; IPR000969 (Structure-specific recognition protein), IPR009071 (High mobility group box domain), IPR011993 (Pleckstrin homology-like domain), IPR013719 (Domain of unknown function DUF1747), IPR024954 (SSRP1 domain); GO:0003677 (DNA binding), GO:0005634 (nucleus) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1963
|
| Description: |
cyclic pyranopterin monophosphate synthase, mitochondrial-like isoform X1 [Glycine max]; IPR007197 (Radical SAM), IPR013483 (Molybdenum cofactor biosynthesis protein A); GO:0003824 (catalytic activity), GO:0006777 (Mo-molybdopterin cofactor biosynthetic process), GO:0019008 (molybdopterin synthase complex), GO:0046872 (metal ion binding), GO:0051536 (iron-sulfur cluster binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
848
|
| Description: |
Signal recognition particle, SRP9/SRP14 subunit; IPR003210 (Signal recognition particle, SRP14 subunit), IPR009018 (Signal recognition particle, SRP9/SRP14 subunit); GO:0006614 (SRP-dependent cotranslational protein targeting to membrane), GO:0008312 (7S RNA binding), GO:0030942 (endoplasmic reticulum signal peptide binding), GO:0048500 (signal recognition particle) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2617
|
| Description: |
elongation factor Tu GTP-binding domain protein; IPR004540 (Translation elongation factor EFG/EF2), IPR005225 (Small GTP-binding protein domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003746 (translation elongation factor activity), GO:0003924 (GTPase activity), GO:0005525 (GTP binding), GO:0005622 (intracellular), GO:0006414 (translational elongation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2331
|
| Description: |
lysine-tRNA ligase-like protein; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004824 (lysine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006430 (lysyl-tRNA aminoacylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3085
|
| Description: |
dual specificity protein phosphatase family protein; IPR000340 (Dual specificity phosphatase, catalytic domain), IPR011009 (Protein kinase-like domain), IPR024950 (Dual specificity phosphatase); GO:0004725 (protein tyrosine phosphatase activity), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2723
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0000151 (ubiquitin ligase complex), GO:0004672 (protein kinase activity), GO:0004842 (ubiquitin-protein ligase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016567 (protein ubiquitination) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1263
|
| Description: |
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN-like [Glycine max]; IPR000008 (C2 domain), IPR014019 (Phosphatase tensin type); GO:0004725 (protein tyrosine phosphatase activity), GO:0005515 (protein binding), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3422
|
| Description: |
Cytochrome C assembly protein; IPR002541 (Cytochrome c assembly protein), IPR003557 (Cytochrome c-type biogenesis protein CcmC); GO:0006461 (protein complex assembly), GO:0008535 (respiratory chain complex IV assembly), GO:0015232 (heme transporter activity), GO:0015886 (heme transport), GO:0016020 (membrane), GO:0017004 (cytochrome complex assembly) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3213
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0000151 (ubiquitin ligase complex), GO:0004672 (protein kinase activity), GO:0004842 (ubiquitin-protein ligase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016567 (protein ubiquitination) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
4867
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR001650 (Helicase, C-terminal), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR025766 (ADD domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003676 (nucleic acid binding), GO:0003677 (DNA binding), GO:0004386 (helicase activity), GO:0005524 (ATP binding) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
912
|
| Description: |
Signal recognition particle, SRP9/SRP14 subunit; IPR003210 (Signal recognition particle, SRP14 subunit), IPR009018 (Signal recognition particle, SRP9/SRP14 subunit); GO:0006614 (SRP-dependent cotranslational protein targeting to membrane), GO:0008312 (7S RNA binding), GO:0030942 (endoplasmic reticulum signal peptide binding), GO:0048500 (signal recognition particle) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2538
|
| Description: |
high mobility group B protein 15-like isoform X7 [Glycine max]; IPR000969 (Structure-specific recognition protein), IPR009071 (High mobility group box domain), IPR011993 (Pleckstrin homology-like domain), IPR013719 (Domain of unknown function DUF1747), IPR024954 (SSRP1 domain); GO:0003677 (DNA binding), GO:0005634 (nucleus) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1960
|
| Description: |
putative dual specificity protein phosphatase DSP8-like isoform X2 [Glycine max]; IPR000340 (Dual specificity phosphatase, catalytic domain), IPR024950 (Dual specificity phosphatase); GO:0004725 (protein tyrosine phosphatase activity), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2954
|
| Description: |
elongation factor Tu GTP-binding domain protein; IPR004540 (Translation elongation factor EFG/EF2), IPR005225 (Small GTP-binding protein domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003746 (translation elongation factor activity), GO:0003924 (GTPase activity), GO:0005525 (GTP binding), GO:0005622 (intracellular), GO:0006414 (translational elongation) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2597
|
| Description: |
aspartate--tRNA ligase, mitochondrial-like isoform X1 [Glycine max]; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0016874 (ligase activity) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1911
|
| Description: |
photosystem I P700 chlorophyll A apoprotein A2; IPR001209 (Ribosomal protein S14), IPR001280 (Photosystem I PsaA/PsaB); GO:0003735 (structural constituent of ribosome), GO:0005622 (intracellular), GO:0005840 (ribosome), GO:0006412 (translation), GO:0009522 (photosystem I), GO:0009579 (thylakoid), GO:0015979 (photosynthesis), GO:0016021 (integral component of membrane) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3042
|
| Description: |
protein kinase family protein; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR024788 (Malectin-like carbohydrate-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2461
|
| Description: |
high mobility group B protein 15-like isoform X7 [Glycine max]; IPR000969 (Structure-specific recognition protein), IPR009071 (High mobility group box domain), IPR011993 (Pleckstrin homology-like domain), IPR013719 (Domain of unknown function DUF1747), IPR024954 (SSRP1 domain); GO:0003677 (DNA binding), GO:0005634 (nucleus) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2371
|
| Description: |
activator of 90 kDa heat shock protein ATPase homolog [Glycine max]; IPR013538 (Activator of Hsp90 ATPase homologue 1-like), IPR015310 (Activator of Hsp90 ATPase, N-terminal), IPR023393 (START-like domain); GO:0001671 (ATPase activator activity), GO:0006950 (response to stress), GO:0051087 (chaperone binding) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3192
|
| Description: |
dual specificity protein phosphatase family protein; IPR000340 (Dual specificity phosphatase, catalytic domain), IPR011009 (Protein kinase-like domain), IPR024950 (Dual specificity phosphatase); GO:0004725 (protein tyrosine phosphatase activity), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2333
|
| Description: |
lysine-tRNA ligase-like protein; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004824 (lysine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006430 (lysyl-tRNA aminoacylation) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1650
|
| Description: |
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN-like [Glycine max]; IPR000008 (C2 domain), IPR014019 (Phosphatase tensin type); GO:0004725 (protein tyrosine phosphatase activity), GO:0005515 (protein binding), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2545
|
| Description: |
folic acid synthesis protein fol1-like isoform X3 [Glycine max]; IPR000550 (7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK), IPR011005 (Dihydropteroate synthase-like); GO:0003848 (2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity), GO:0004156 (dihydropteroate synthase activity), GO:0009396 (folic acid-containing compound biosynthetic process), GO:0042558 (pteridine-containing compound metabolic process), GO:0044237 (cellular metabolic process) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3236
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0000151 (ubiquitin ligase complex), GO:0004672 (protein kinase activity), GO:0004842 (ubiquitin-protein ligase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016567 (protein ubiquitination) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2499
|
| Description: |
asparagine synthetase domain-containing protein 1-like isoform X4 [Glycine max]; IPR000583 (Class II glutamine amidotransferase domain), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold), IPR017932 (Glutamine amidotransferase type 2 domain); GO:0004066 (asparagine synthase (glutamine-hydrolyzing) activity), GO:0006529 (asparagine biosynthetic process), GO:0008152 (metabolic process) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
357
|
| Description: |
glycyl-tRNA synthetase / glycine--tRNA ligase; IPR002314 (Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain), IPR027031 (Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0005524 (ATP binding), GO:0006418 (tRNA aminoacylation for protein translation) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2690
|
| Description: |
elongation factor Tu GTP-binding domain protein; IPR004540 (Translation elongation factor EFG/EF2), IPR005225 (Small GTP-binding protein domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003746 (translation elongation factor activity), GO:0003924 (GTPase activity), GO:0005525 (GTP binding), GO:0005622 (intracellular), GO:0006414 (translational elongation) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1550
|
| Description: |
activator of 90 kDa heat shock protein ATPase homolog [Glycine max]; IPR013538 (Activator of Hsp90 ATPase homologue 1-like), IPR015310 (Activator of Hsp90 ATPase, N-terminal), IPR023393 (START-like domain); GO:0001671 (ATPase activator activity), GO:0006950 (response to stress), GO:0051087 (chaperone binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2940
|
| Description: |
high mobility group B protein 15-like isoform X7 [Glycine max]; IPR000969 (Structure-specific recognition protein), IPR009071 (High mobility group box domain), IPR011993 (Pleckstrin homology-like domain), IPR013719 (Domain of unknown function DUF1747), IPR024954 (SSRP1 domain); GO:0003677 (DNA binding), GO:0005634 (nucleus) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
4878
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR001650 (Helicase, C-terminal), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR025766 (ADD domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003676 (nucleic acid binding), GO:0003677 (DNA binding), GO:0004386 (helicase activity), GO:0005524 (ATP binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3073
|
| Description: |
protein kinase family protein; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR024788 (Malectin-like carbohydrate-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2493
|
| Description: |
folic acid synthesis protein fol1-like isoform X3 [Glycine max]; IPR000550 (7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK), IPR011005 (Dihydropteroate synthase-like); GO:0003848 (2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity), GO:0004156 (dihydropteroate synthase activity), GO:0009396 (folic acid-containing compound biosynthetic process), GO:0042558 (pteridine-containing compound metabolic process), GO:0044237 (cellular metabolic process) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1956
|
| Description: |
asparagine synthetase domain-containing protein 1-like isoform X4 [Glycine max]; IPR000583 (Class II glutamine amidotransferase domain), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold), IPR017932 (Glutamine amidotransferase type 2 domain); GO:0004066 (asparagine synthase (glutamine-hydrolyzing) activity), GO:0006529 (asparagine biosynthetic process), GO:0008152 (metabolic process) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1652
|
| Description: |
phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN-like [Glycine max]; IPR000008 (C2 domain), IPR014019 (Phosphatase tensin type); GO:0004725 (protein tyrosine phosphatase activity), GO:0005515 (protein binding), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3097
|
| Description: |
elongation factor Tu GTP-binding domain protein; IPR004540 (Translation elongation factor EFG/EF2), IPR005225 (Small GTP-binding protein domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003746 (translation elongation factor activity), GO:0003924 (GTPase activity), GO:0005525 (GTP binding), GO:0005622 (intracellular), GO:0006414 (translational elongation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3042
|
| Description: |
protein kinase family protein; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR024788 (Malectin-like carbohydrate-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2321
|
| Description: |
lysine-tRNA ligase-like protein; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004824 (lysine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006430 (lysyl-tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2756
|
| Description: |
aspartate--tRNA ligase, mitochondrial-like isoform X1 [Glycine max]; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0016874 (ligase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
4864
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR001650 (Helicase, C-terminal), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR025766 (ADD domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003676 (nucleic acid binding), GO:0003677 (DNA binding), GO:0004386 (helicase activity), GO:0005524 (ATP binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1599
|
| Description: |
activator of 90 kDa heat shock protein ATPase homolog [Glycine max]; IPR013538 (Activator of Hsp90 ATPase homologue 1-like), IPR015310 (Activator of Hsp90 ATPase, N-terminal), IPR023393 (START-like domain); GO:0001671 (ATPase activator activity), GO:0006950 (response to stress), GO:0051087 (chaperone binding) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2402
|
| Description: |
activator of 90 kDa heat shock protein ATPase homolog [Glycine max]; IPR013538 (Activator of Hsp90 ATPase homologue 1-like), IPR015310 (Activator of Hsp90 ATPase, N-terminal), IPR023393 (START-like domain); GO:0001671 (ATPase activator activity), GO:0006950 (response to stress), GO:0051087 (chaperone binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
285
|
| Description: |
serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like isoform X1 [Glycine max]; IPR000009 (Protein phosphatase 2A, regulatory subunit PR55); GO:0000159 (protein phosphatase type 2A complex), GO:0007165 (signal transduction), GO:0008601 (protein phosphatase type 2A regulator activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2479
|
| Description: |
high mobility group B protein 15-like isoform X7 [Glycine max]; IPR000969 (Structure-specific recognition protein), IPR009071 (High mobility group box domain), IPR011993 (Pleckstrin homology-like domain), IPR013719 (Domain of unknown function DUF1747), IPR024954 (SSRP1 domain); GO:0003677 (DNA binding), GO:0005634 (nucleus) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2021
|
| Description: |
putative dual specificity protein phosphatase DSP8-like isoform X2 [Glycine max]; IPR000340 (Dual specificity phosphatase, catalytic domain), IPR024950 (Dual specificity phosphatase); GO:0004725 (protein tyrosine phosphatase activity), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3200
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0000151 (ubiquitin ligase complex), GO:0004672 (protein kinase activity), GO:0004842 (ubiquitin-protein ligase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016567 (protein ubiquitination) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3583
|
| Description: |
elongation factor Tu GTP-binding domain protein; IPR004540 (Translation elongation factor EFG/EF2), IPR005225 (Small GTP-binding protein domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003746 (translation elongation factor activity), GO:0003924 (GTPase activity), GO:0005525 (GTP binding), GO:0005622 (intracellular), GO:0006414 (translational elongation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1571
|
| Description: |
activator of 90 kDa heat shock protein ATPase homolog [Glycine max]; IPR013538 (Activator of Hsp90 ATPase homologue 1-like), IPR015310 (Activator of Hsp90 ATPase, N-terminal), IPR023393 (START-like domain); GO:0001671 (ATPase activator activity), GO:0006950 (response to stress), GO:0051087 (chaperone binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2367
|
| Description: |
activator of 90 kDa heat shock protein ATPase homolog [Glycine max]; IPR013538 (Activator of Hsp90 ATPase homologue 1-like), IPR015310 (Activator of Hsp90 ATPase, N-terminal), IPR023393 (START-like domain); GO:0001671 (ATPase activator activity), GO:0006950 (response to stress), GO:0051087 (chaperone binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2015
|
| Description: |
putative dual specificity protein phosphatase DSP8-like isoform X2 [Glycine max]; IPR000340 (Dual specificity phosphatase, catalytic domain), IPR024950 (Dual specificity phosphatase); GO:0004725 (protein tyrosine phosphatase activity), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2469
|
| Description: |
high mobility group B protein 15-like isoform X7 [Glycine max]; IPR000969 (Structure-specific recognition protein), IPR009071 (High mobility group box domain), IPR011993 (Pleckstrin homology-like domain), IPR013719 (Domain of unknown function DUF1747), IPR024954 (SSRP1 domain); GO:0003677 (DNA binding), GO:0005634 (nucleus) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3152
|
| Description: |
dual specificity protein phosphatase family protein; IPR000340 (Dual specificity phosphatase, catalytic domain), IPR011009 (Protein kinase-like domain), IPR024950 (Dual specificity phosphatase); GO:0004725 (protein tyrosine phosphatase activity), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2511
|
| Description: |
folic acid synthesis protein fol1-like isoform X3 [Glycine max]; IPR000550 (7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK), IPR011005 (Dihydropteroate synthase-like); GO:0003848 (2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity), GO:0004156 (dihydropteroate synthase activity), GO:0009396 (folic acid-containing compound biosynthetic process), GO:0042558 (pteridine-containing compound metabolic process), GO:0044237 (cellular metabolic process) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
972
|
| Description: |
Signal recognition particle, SRP9/SRP14 subunit; IPR003210 (Signal recognition particle, SRP14 subunit), IPR009018 (Signal recognition particle, SRP9/SRP14 subunit); GO:0006614 (SRP-dependent cotranslational protein targeting to membrane), GO:0008312 (7S RNA binding), GO:0030942 (endoplasmic reticulum signal peptide binding), GO:0048500 (signal recognition particle) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2720
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0000151 (ubiquitin ligase complex), GO:0004672 (protein kinase activity), GO:0004842 (ubiquitin-protein ligase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016567 (protein ubiquitination) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1731
|
| Description: |
probable protein phosphatase 2C 42-like [Glycine max]; IPR001932 (Protein phosphatase 2C (PP2C)-like domain), IPR006869 (Domain of unknown function DUF547), IPR015655 (Protein phosphatase 2C), IPR016161 (Aldehyde/histidinol dehydrogenase); GO:0003824 (catalytic activity), GO:0008152 (metabolic process), GO:0016491 (oxidoreductase activity), GO:0055114 (oxidation-reduction process) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Glycosyl transferase, family 35 |
| Type: |
Family |
| Description: |
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.Glycosyltransferase family 35
comprises enzymes with only one known activity; glycogen and starch phosphorylase ().
The main role of glycogen phosphorylase (GPase) is to provide phosphorylated glucose molecules (G-1-P) [
]. GPase is a highly regulated allosteric enzyme. The net effect of the regulatory site allows the enzyme to operate at a variety of rates; the enzyme is not simply regulated as "on"or "off", but rather it can be thought of being set to operate at an ideal rate based on changing conditions at in the cell. The most important allosteric effector is the phosphate molecule covalently attached to Ser14.
This switches GPase from the b (inactive) state to the a (active) state. Upon phosphorylation, GPase attains about 80% of its Vmax. When the enzyme is not phosphorylated, GPase activity is practically non-existent at low AMP levels.There is some apparent controversy as to the structure of GPase. All sources agree that the enzyme is multimeric, but there is apparent controversy as to the enzyme being a tetramer or a dimer. Apparently, GPase (in the aform) forms tetramers in the crystal form. The consensus seems to be that `regardless of the a or b form, GPase functions as a dimer
in vivo[
]. The GPase monomer is best described as consisting of two domains, an N-terminal domain and a C-terminal domain []. The C-terminal domain is often referred to as the catalytic domain. It consists of a β-sheet core surrounded by layers of helical segments []. The vitamin cofactor pyridoxal phosphate (PLP) is covalently attached to the amino acid backbone. The N-terminal domain also consists of a central β-sheet core and is surrounded by layers of helical segments. The N-terminal domain contains different allosteric effector sites to regulate the enzyme.Bacterial phosphorylases follow the same catalytic mechanisms as their plant and animal counterparts, but differ considerably in terms of their substrate specificity and regulation. The catalytic domains are highly conserved while the regulatory sites are only poorly conserved. For maltodextrin phosphorylase from Escherichia coli the physiological role of the enzyme in the utilisation of maltidextrins is known in detail; that of all the other bacterial phosphorylases is still unclear. Roles in regulatuon of endogenous glycogen metabolism in periods of starvation, and sporulation, stress response or quick adaptation to changing environments are possible [
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
ATP synthase, F0 complex, subunit B/MI25 |
| Type: |
Family |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.This entry represents subunit B from the F0 complex in F-ATPases found in mitochondria of eukaryotes (known as ATP4 in yeast [
] and MI25/ORF25 in plants []). The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
ADP-L-glycero-D-manno-heptose-6-epimerase |
| Type: |
Family |
| Description: |
Lipopolysaccharides (LPS) are glycolipids that consitutes the outer monolayer of the outer membranes of most Gram-negative bacteria [
]. They consist of lipid A (endotoxin) which anchors LPS to the outer membrane, a non-repeating core oligosachharide, and an immunogenic O-antigen repeat polymer, which is an oligosaccharide of 1-40 units that variesbetween different strains of bacteria. Although the O-antigen and most of the core domain are not necessary for growth in the lab, they appear to help bacteria resist environmental stresses including the complement system and antibiotics.This family consists of examples of ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme involved in biosynthesis of the inner core of LPS in Gram-negative bacteria [
]. This enzyme is homologous to UDP-glucose 4-epimerase () and belongs to the NAD dependent epimerase/dehydratase family. It participates in the biosynthetic pathway leading to incorporation of heptose, a conserved sugar, into the core region of LPS, performing the NAD-dependent reaction shown below:
ADP-D-glycero-D-manno-heptose = ADP-L-glycero-D-manno-heptoseIt is a homopentameric enzyme with each monomer composed of two domains: an N-terminal modified Rossman fold domain for NADP binding, and a C-terminal substrate binding domain. This subgroup has the canonical active site tetrad and NAD(P)-binding motif [].Extended short-chain dehydrogenases/reductases (SDRs) are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central β-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG].XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif [
,
,
,
,
,
,
,
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Bacterial/eukaryotic lysine-tRNA ligase, class II |
| Type: |
Family |
| Description: |
This entry represents a conserved group of class II lysine-tRNA ligases from eukaryotes and bacteria.Lysine-tRNA synthesis is catalysed by two unrelated families of tRNA ligases: class-I or class-II. In eubacteria and eukaryota lysine-tRNA ligases belong to class II, the same family as aspartyl tRNA ligase. The lysine-tRNA ligase class Ic family is present in archaea and some eubacteria [
]. Moreover in some eubacteria there is a gene X, which is similar to a part of lysine-tRNA ligase from class II.Lysine-tRNA ligase is duplicated in some species with, for example in Escherichia coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots"of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [
].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c []. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Glycine-tRNA ligase, archaeal |
| Type: |
Family |
| Description: |
This entry represents archaeal glycine-tRNA ligases (also known as glycyl-tRNA synthetases).In eubacteria, glycine-tRNA ligase (
) is an α2/β2 tetramer composed of 2 different subunits [
,
,
]. In some eubacteria, in archaea and eukaryota, glycine-tRNA ligase is an α2 dimer, this family. It belongs to class IIc and is one of the most complex ligases. What is most interesting is the lack of similarity between the two types: divergence at the sequencelevel is so great that it is impossible to infer descent from common genes. The alpha (see
) and beta subunits (see
) also lack significant sequence similarity. However, they are translated from a single mRNA [
], and a single chain glycine-tRNA ligase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain [
].The sequence and crystal structure of the homodimeric glycine-tRNA ligase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel β-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA ligase due to the conserved nature of the class II active site [
,
].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c []. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Glycine-tRNA ligase, bacterial |
| Type: |
Family |
| Description: |
This entry represents bacterial Glycine-tRNA ligases (also known as Glycyl-tRNA synthetase).In eubacteria, glycine-tRNA ligase (
) is an α2/β2 tetramer composed of 2 different subunits [
,
,
]. In some eubacteria, in archaea and eukaryota, glycine-tRNA ligase is an α2 dimer, this family. It belongs to class IIc and is one of the most complex ligases. What is most interesting is the lack of similarity between the two types: divergence at the sequencelevel is so great that it is impossible to infer descent from common genes. The alpha (see
) and beta subunits (see
) also lack significant sequence similarity. However, they are translated from a single mRNA [
], and a single chain glycine-tRNA ligase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain [
].The sequence and crystal structure of the homodimeric glycine-tRNA ligase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel β-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA ligase due to the conserved nature of the class II active site [
,
].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
5-Hydroxytryptamine 2A receptor |
| Type: |
Family |
| Description: |
5-hydroxytryptamine (5-HT) or serotonin, is a neurotransmitter that it is primarily found in the gastrointestinal (GI) tract, platelets, and in the central nervous system (CNS). It is implicated in a vast array of physiological and pathophysiological pathways. Receptors for 5-HT mediate both excitatory and inhibitory neurotransmission, and modulate the release of many neurotransmitters including glutamate, GABA, dopamine, epinephrine/norepinephrine, and acetylcholine, as well as many hormones, including oxytocin, prolactin, vasopressin and cortisol. In the CNS, 5-HT receptors can influence various neurological processes, such as aggression, anxiety and appetite and, as a, result are the target of a variety of pharmaceutical drugs, including many antidepressants, antipsychotics and anorectics [
]. The 5-HT receptors are grouped into a number of distinct subtypes, classified according to their antagonist susceptibilities and their affinities for 5-HT. With the exception of the 5-HT3 receptor, which is a ligand-gated ion channel [
], all 5-HT receptors are members of the rhodopsin-like G protein-coupled receptor family [], and they activate an intracellular second messenger cascade to produce their responses. The 5-HT2 receptors mediate many of the central and peripheral physiologic functions of 5-hydroxytryptamine. The original 5HT2 receptor (now renamed as the 5-HT2A receptor) was initially classified according to its ability to display micromolar affinity for 5-HT, to be labelled with [3H]spiperone and by its susceptibility to 5-HT antagonists. At least 3 members of the 5HT2 receptor subfamily exist (5-HT2A, 5-HT2B, 5-HT2C), all of which share a high degree of sequence similarity and couple to Gq/G11 to stimulate the phosphoinositide pathway and elevate cytosolic calcium. Cardiovascular effects include contraction of blood vessels and shape changes in platelets; central nervous system effects include neuronal sensitisation to tactile stimuli and mediation of some of the effects of phenylisopropylamine hallucinogens. 5-HT2 receptors display functional selectivity in which the same agonist in different cell types or different agonists in the same cell type can differentially activate multiple, distinct signalling pathways [].This entry represents the 5-HT2A receptor (previously classified just as 5-HT2), which is one of the main excitatory serotonin receptors. It is expressed throughout the central nervous system [
,
] with high concentrations found on the apical dendrites of pyramidal cells in layer V of the cortex [,
,
], which are thought to modulate cognitive processes by enhancing glutamate release followed by a complex range of interactions with the 5-HT1A [], GABAA [], adenosine A1 [], AMPA [], mGluR2/3 [], mGlu5 [] and OX2 receptors []. In the periphery, the 5-HT2A receptor is highly expressed in platelets and many cell types of the cardiovascular system, in fibroblasts, and in neurons of the peripheral nervous system. Additionally, 5-HT2A mRNA expression has been observed in human monocytes [], and platelet aggregation [] with increased capillary permeability following exposure to 5-HT have been attributed to 5-HT2A receptor-mediated functions. 5-HT2A receptors also mediate contractile responses in a series of vascular smooth muscle preparations [] and activation in hypothalamus causes increases in hormonal levels of oxytocin, prolactin, ACTH, corticosterone, and renin []. |
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| Protein Domain |
| Name: |
ATP synthase, F0 complex, subunit B |
| Type: |
Family |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.This entry represents subunit B from the F0 complex in F-ATPases found in mitochondria of metazoans and fungi. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D [
]. |
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| Protein Domain |
| Name: |
Lysine-tRNA ligase, class II, N-terminal |
| Type: |
Domain |
| Description: |
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].Lysine-tRNA synthesis is catalysed by two unrelated families of tRNA ligases: class-I or class-II. In eubacteria and eukaryota lysine-tRNA ligases belong to class II, the same family as aspartyl tRNA ligase. The lysine-tRNA ligase class Ic family is present in archaea and some eubacteria [
]. Moreover in some eubacteria there is a gene X, which is similar to a part of lysine-tRNA ligase from class II.Lysine-tRNA ligase is duplicated in some species with, for example in Escherichia coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots"of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [
].This entry represents the N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). This domain is a β-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop []. |
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| Protein Domain |
| Name: |
ATP synthase, F0 complex, subunit MI25, plants |
| Type: |
Family |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.This entry represents subunit B from the F0 complex in F-ATPases found in mitochondria of eukaryotes (known as MI25/ORF25 in plants [
]). The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. |
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| Protein Domain |
| Name: |
ATP synthase, F0 complex, subunit D, mitochondrial |
| Type: |
Family |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.This entry represents subunit D from the F0 complex in F-ATPases found in mitochondria. The D subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D [
]. There is no homologue of subunit D in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. |
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| Protein Domain |
| Name: |
ATPase, OSCP/delta subunit |
| Type: |
Family |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.This family represents subunits called delta in bacterial and chloroplast ATPase, or OSCP (oligomycin sensitivity conferral protein) in mitochondrial ATPase (note that in mitochondria there is a different delta subunit,
). The OSCP/delta subunit appears to be part of the peripheral stalk that holds the F1 complex alpha3beta3 catalytic core stationary against the torque of the rotating central stalk, and links subunit A of the F0 complex with the F1 complex. In mitochondria, the peripheral stalk consists of OSCP, as well as F0 components F6, B and D. In bacteria and chloroplasts the peripheral stalks have different subunit compositions: delta and two copies of F0 component B (bacteria), or delta and F0 components B and B' (chloroplasts) [
,
]. |
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| Protein Domain |
| Name: |
DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type |
| Type: |
Homologous_superfamily |
| Description: |
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo IB; eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB [
]. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [,
]. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases [,
].This superfamily represents the α-helical subdomain that comprises part of the catalytic core of eukaryotic and viral topoisomerase I (type IB) enzymes, which occurs near the C-terminal region of the protein.Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity [
]. The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps"around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes [
].Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. The crystal structure of an amino-terminal fragment of vaccinia virus DNA topoisomerase I shows that the fragment forms a five-stranded, antiparallel β-sheet with two short α-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure [
]. |
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| Protein Domain |
| Name: |
DNA topoisomerase I, catalytic core, eukaryotic-type |
| Type: |
Domain |
| Description: |
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo IB; eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB [
]. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [,
]. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases [,
].This entry represents the catalytic core of eukaryotic and viral topoisomerase I (type IB) enzymes, which occurs near the C-terminal region of the protein.Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity [
]. The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps"around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes [
].Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. The crystal structure of an amino-terminal fragment of vaccinia virus DNA topoisomerase I shows that the fragment forms a five-stranded, antiparallel β-sheet with two short α-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure [
]. |
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| Protein Domain |
| Name: |
Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family |
| Type: |
Family |
| Description: |
Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see [].Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways [
].There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different [
].The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria. The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified. The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana. The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum. Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways.2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (also known as tetrahydrodipicolinate N-succinyltransferase or DapD) is part of the succinyl route of of lysine/DAP biosynthesis. The DapD protein is a homotrimer is a trimeric enzyme with each monomer composed of three domain: an N-terminal helical domain, a distinctive left-handed parallel β-helix (LBH) domain, and a predominantly beta C-terminal domain [
,
]. The LBH structure is encoded by an imperfect tandem-repeated hexapeptide sequence. Each trimer contains three independent active sites, always occuring at the boundary of two subunits, and formed by residues from one N-terminal domain, one C-terminal domain and two adjacent LBH domains. |
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| Protein Domain |
| Name: |
Glucose transporter, type 3 (GLUT3) |
| Type: |
Family |
| Description: |
The ability to transport glucose across the plasma membrane is a feature common to nearly all cells, from simple bacteria through to highly specialised mammalian neurones. Facilitative sugar transport is mediated by members of the GLUT transporter family, which form an aqueous pore across the membrane through which sugars can move in a passive (i.e., energy-independent) manner; in consequence, they can only transport sugars down their concentration gradient. The GLUT family of glycosylated transmembrane proteins are predicted to span the membrane 12 times with both amino- and carboxyl-termini located in the cytosol. On the basis of sequence homology and structural similarity, three subclasses of sugar transporters have been defined: Class I (GLUTs 1-4) are glucose transporters; Class II (GLUTs 5, 7, 9 and 11) are fructose transporters; and Class III (GLUTs 6, 8, 10, 12 and HMIT1) are structurally atypical members of the GLUT family, which are poorly defined at present, indeed GLUT6 may only be a pseudo-gene [
,
,
,
,
].The confirmed isoforms are expressed in a tissue and cell-specific manner, and exhibit distinct kinetic and regulatory properties, presumably reflecting their specific functional roles. They belong to a much larger 'major facilitator superfamily' of 12 TM transporters that are involved in the transport of a variety of hexoses and other carbon compounds, and include: bacterial sugar-proton symporters (H
+/xylose and H
+/arabinose); bacterial transporters of carboxylic acids and antibiotics; and sugar transporters in various yeast, protozoa and higher plants. Nevertheless, amino acid identity within the superfamily may be as low as ~25% [
,
]. Besides the 12 presumed TM domains, the most characteristic structural feature of the superfamily is a five residue motif (RXGRR, where X is any amino acid). In the GLUT transporters, this motif is present in the presumed cytoplasmic loops connecting TM domains 2 with 3, and also 8 with 9. The 12 TM transporter superfamily appears to be structurally unrelated to the Na+-coupled, Na
+/glucose co-transporters (SGLT1-3) found in the intestine and kidney, which are able to transport glucose against its concentration gradient [
].Comparison of the hydropathy profiles for GLUT1-5 reveals that they are virtually superimposable, despite the fact that their primary structures may differ by up to 60%. Of the presumed TM domains, the fourth, fifth and sixth are the most highly conserved, and conserved residues are also found in the short exofacial loops joining the putative TM regions. The presumed cytoplasmic N- and C-termini, and the extracellular loop between the first and second TM domains, show the greatest divergence, both in terms of primary structure and size.GLUT3 is the most prominent glucose transporter isoform expressed in adult
brain, where it tends to be preferentially located in neurones, ratherthan in other cell types, such as glia or endothelial cells. It is also
widely distributed in other human tissues, having been detected in theliver, kidney and placenta. In other species, it shows a more restricted
expression pattern. It consists of 496 amino acids (human isoform) andshares 64% amino acid identity with GLUT1 and 52% with GLUT2. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, thumb domain, birnavirus |
| Type: |
Domain |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents the thumb domain of RdRp from Birnavirus, which contain the conserved RdRp motifs that reside in the catalytic "palm"domain (
) of all classes of polymerases but in a characteristic permuted order, thus, it adopts a unique active site topology [
,
]. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [,
,
]. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus |
| Type: |
Homologous_superfamily |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents the thumb domain of RdRp from Birnavirus, which contain the conserved RdRp motifs that reside in the catalytic "palm"domain (
) of all classes of polymerases but in a characteristic permuted order, thus, it adopts a unique active site topology [
,
]. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps [,
,
]. This domain adopts an α-helical bundle arrangement. |
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| Protein Domain |
| Name: |
Glycine receptor alpha |
| Type: |
Family |
| Description: |
Glycine is a major inhibitory neurotransmitter (NT) in the adult vertebrate
central nervous system (CNS). Glycinergic synapses have a well-establishedrole in the processing of motor and sensory information that controls
movement, vision and audition []. This action of glycine is mediatedthrough its interaction with the glycine receptor (GlyR): an intrinsic
chloride channel is opened in response to agonist binding. The subsequentinflux of anions prevents membrane depolarisation and neuronal firing
induced by excitatory NTs. Strychnine acts as a competitive antagonist ofglycine binding, thereby reducing the activity of inhibitory neurones.
Poisoning with strychnine is characterised by over-excitation, muscle spasmsand convulsions. Whilst glycine is the principal physiological agonist at
GlyRs, taurine and beta-alanine also behave as agonists []. Compounds thatmodulate GlyR activity include zinc, some alcohols and anaesthetics,
picrotoxin, cocaine and some anticonvulsants. GlyRs were thought for sometime to be localised exclusively in the brain stem and spinal cord, but have
since been found to be expressed more widely, including the cochlear nuclei,cerebellar cortex and forebrain [
].GlyRs belong to the ligand-gated ion channel family, which also includes the
inhibitory gamma-aminobutyric acid type A (GABAA) and excitatory nicotinicacetylcholine (nACh) and serotonin type 3 (5-HT3) receptors [
].Affinity-purified GlyR was found to contain two glycosylated membrane
proteins of 48kDa and 56kDa, corresponding to alpha and beta subunits,respectively. Four genes encoding alpha subunits have been identified (GLRA1
to 4), together with a single beta polypeptide (GLRB). The heterogeneity ofalpha subunits is further increased by alternative exon splicing, yielding
two isoforms of GLRA1 to 3 []. The characteristics of different GlyRsubtypes, therefore, can be largely explained by their GLRA content.
GlyRs are generally believed to adopt a pentameric structure in vivo: five
subunits assemble to form a ring structure with a central pore. Typically, astoichiometry of 3:2 (alpha:beta) is observed [
]. GlyR subunits share ahigh overall level of sequence similarity both with themselves and with the
subunits of the GABAA and nACh receptors. Four highly conserved segmentshave been proposed to correspond to transmembrane (TM) α-helices (TM1-4),
the second of which is thought to contribute to the pore wall []. A long extracellular N-terminal segment precedes TM1 and a long cytoplasmic loop
links TM3 and 4. Short cytoplasmic and extracellular loops join TM1-2 andTM2-3, respectively, and a short C-terminal sequence follows TM4. Studies
using radiolabelled strychnine have shown the alpha subunit to beresponsible for ligand binding, the critical residues for this interaction
lying within the N-terminal domain. The beta subunit plays a structuralrole, contributing one of its TM domains to the pore wall as well as playing
a putative role in postsynaptic clustering of the receptor.In several mammalian species, defects in glycinergic transmission are
associated with complex motor disorders. Mutations in the gene encodingGLRA1 give rise to hyperplexia, or startle disease [
]. This ischaracterised by muscular spasms in response to unexpected light or noise
stimuli, similar to the symptoms of sublethal doses of strychnine. Themutations result in amino acid substitutions within the TM1-2 and TM3-4
loops, suggesting that these regions are involved in the transduction ofligand binding into channel activation.
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| Protein Domain |
| Name: |
5-hydroxytryptamine 3 receptor |
| Type: |
Family |
| Description: |
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [
,
]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [
].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [
].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [
].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [
].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [
,
].Serotonin (5-hydroxytryptamine, 5-HT) is widely distributed in both the central and peripheral nervous system, where it acts as a neurotransmitter
and neuromodulator []. It has been implicated in several aspects of brain function, including regulation of affective states, ingestive behavior and addiction. 5-HT can activate a number of different receptor subtypes that produce diverse neuronal responses, principally through activation of G-protein-mediated signalling pathways. Signalling through the 5-HT3 receptor (5-HT3R) differs, since this subtype belongs to the ligand-gated ion channel (LGIC) superfamily, which also includes the inhibitory gamma-aminobutyric acid type A and glycine receptors, and excitatory nicotinic acetylcholine receptors (nAChR) []. 5-HT3 receptor function has been implicated in a variety of neural processes, including pain perception, emesis, anxiety and drug abuse.Like the other members of the LGIC superfamily, the 5HT3R exhibits a high degree of sequence similarity, and therefore putative structural similarity, with nAChRs [
]. Thus, functional 5HT3Rs comprise a pentamer: the ion channel is formed at the centre of a rosette formed between five homologous subunits. Two classes of 5-HT3R subunit are currently known, termed 5-HT3A and 5-HT3B. Whilst homomeric pentamers of 5-HT3A form functional receptors, heteromeric assemblies display channel conductances, cation permeabilities and current-voltage relationships typical of characterised neuronal 5-HT3 channels [].The proposed topology of 5-HT3R subunits comprises four putative transmembrane (TM) domains (designated M1-4); a large extracellular N-terminal region (~200 amino acids); and a variable cytoplasmic loop between M3 and M4. The M2 domains from each subunit are thought to form the channel pore. The agonist binding site is formed by the N terminus, which, on binding, induces a conformational change in the channel pore, a process often referred to as "gating"[
]. Opening of the pore allows cation flux through the neuronal membrane and depolarises the membrane potential. Thus, 5-HT3Rs may be thought of as excitatory receptors []. |
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| Protein Domain |
| Name: |
ATP synthase-coupling factor 6, mitochondrial |
| Type: |
Family |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D [
]. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. |
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1322
|
| Description: |
endonuclease III-like protein 1-like isoform X2 [Glycine max]; IPR005759 (Endonuclease III), IPR011257 (DNA glycosylase), IPR023170 (Helix-turn-helix, base-excision DNA repair, C-terminal); GO:0003677 (DNA binding), GO:0003824 (catalytic activity), GO:0003906 (DNA-(apurinic or apyrimidinic site) lyase activity), GO:0006281 (DNA repair), GO:0006284 (base-excision repair) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3337
|
| Description: |
respiratory burst oxidase protein F; IPR000778 (Cytochrome b245, heavy chain), IPR011992 (EF-hand domain pair), IPR013130 (Ferric reductase transmembrane component-like domain), IPR017938 (Riboflavin synthase-like beta-barrel); GO:0004601 (peroxidase activity), GO:0005509 (calcium ion binding), GO:0016020 (membrane), GO:0016491 (oxidoreductase activity), GO:0055114 (oxidation-reduction process) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
5109
|
| Description: |
clathrin heavy chain 2-like [Glycine max]; IPR016341 (Clathrin, heavy chain); GO:0005198 (structural molecule activity), GO:0005488 (binding), GO:0005515 (protein binding), GO:0006886 (intracellular protein transport), GO:0016192 (vesicle-mediated transport), GO:0030130 (clathrin coat of trans-Golgi network vesicle), GO:0030132 (clathrin coat of coated pit) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
4973
|
| Description: |
RING finger and CHY zinc finger domain-containing protein 1-like isoform X2 [Glycine max]; IPR004039 (Rubredoxin-type fold), IPR008913 (Zinc finger, CHY-type), IPR012312 (Haemerythrin/HHE cation-binding motif), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR017921 (Zinc finger, CTCHY-type); GO:0005515 (protein binding), GO:0008270 (zinc ion binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1883
|
| Description: |
Cysteinyl-tRNA synthetase, class Ia family protein; IPR009080 (Aminoacyl-tRNA synthetase, class 1a, anticodon-binding), IPR024909 (Cysteinyl-tRNA synthetase/mycothiol ligase); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004817 (cysteine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006423 (cysteinyl-tRNA aminoacylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2577
|
| Description: |
tRNA wybutosine-synthesizing protein 1 homolog [Glycine max]; IPR001094 (Flavodoxin), IPR007197 (Radical SAM), IPR013785 (Aldolase-type TIM barrel), IPR013917 (tRNA wybutosine-synthesis); GO:0003824 (catalytic activity), GO:0005506 (iron ion binding), GO:0010181 (FMN binding), GO:0016491 (oxidoreductase activity), GO:0051536 (iron-sulfur cluster binding), GO:0055114 (oxidation-reduction process) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
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•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
5983
|
| Description: |
clathrin heavy chain 2-like [Glycine max]; IPR016341 (Clathrin, heavy chain); GO:0005198 (structural molecule activity), GO:0005488 (binding), GO:0005515 (protein binding), GO:0006886 (intracellular protein transport), GO:0016192 (vesicle-mediated transport), GO:0030130 (clathrin coat of trans-Golgi network vesicle), GO:0030132 (clathrin coat of coated pit) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
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•
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3854
|
| Description: |
Protein kinase superfamily protein; IPR001611 (Leucine-rich repeat), IPR003591 (Leucine-rich repeat, typical subtype), IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR025875 (Leucine rich repeat 4); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
•
•
•
•
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1054
|
| Description: |
urease accessory protein G; IPR012202 ([NiFe]-hydrogenase/urease maturation factor, Ni2-binding GTPase), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003924 (GTPase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006184 (GTP catabolic process), GO:0016151 (nickel cation binding), GO:0016530 (metallochaperone activity), GO:0042803 (protein homodimerization activity) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
4343
|
| Description: |
Protein kinase superfamily protein; IPR001611 (Leucine-rich repeat), IPR003591 (Leucine-rich repeat, typical subtype), IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR025875 (Leucine rich repeat 4); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
•
•
•
•
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2044
|
| Description: |
homeobox-leucine zipper protein HAT4 [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR006712 (HD-ZIP protein, N-terminal), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
•
•
•
•
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| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1900
|
| Description: |
prolyl-tRNA synthetase family protein; IPR002316 (Proline-tRNA ligase, class IIa), IPR017449 (Prolyl-tRNA synthetase, class II); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004827 (proline-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006433 (prolyl-tRNA aminoacylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
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•
•
•
•
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