DNA-directed DNA polymerase, family B, exonuclease domain
Type:
Domain
Description:
DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the
most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases )
by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNAchain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins
may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these aremediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation.
A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regionsof similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I)
includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggestedthat it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and
possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain,and binding domains for both dNTP's and pyrophosphate [
]. This domain is the exonuclease domain of family B DNA polymerases. It adopts a ribonuclease H type fold [
].
DNA-directed DNA polymerase, family B, multifunctional domain
Type:
Domain
Description:
DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases
) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation.
A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. The DNA polymerase structure resembles a right hand with fingers, palm, and thumb, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb [
,
,
].This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [
].
DNA is the biological information that instructs cells how to exist in an
ordered fashion: accurate replication is thus one of the most importantevents in the life cycle of a cell. This function is performed by DNA-
directed DNA-polymerases () by adding nucleotide triphosphate (dNTP) residues
to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain
elongation, although terminal proteins may also be used for the de novosynthesis of a DNA chain.
Even though there are 2 different methods of priming, these are mediated by 2 very similar
polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped
under the designation of DNA polymerase family B.Six regions of similarity (numbered from I to VI) are found in all or a subset
of the B family polymerases. The most conserved region (I) includes a conservedtetrapeptide with two aspartate residues. Its function is not yet known.
However, it has been suggested [] that it may be involved in binding amagnesium ion. All sequences in the B
family contain a characteristic DTDS motif, and possess many functionaldomains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [
],a DNA binding domain, and binding domains for both dNTP's and pyrophosphate [
].
This family consists of chloroplast encoded Ycf2, which is around 2000 residues in length. The function of Ycf2 is unknown, though it may be an ATPase. Its retention in reduced chloroplast genomes of non-photosynthetic plants, e.g. Epifagus virginiana (Beechdrops), and transformation experiments in tobacco indicate that it has an essential function which is probably not related to photosynthesis [
].
This entry contains proteins involved in transport from the ER to the Golgi apparatus as well as in intra-Golgi transport. The Golgi SNAP receptor complex subunit 1 interacts with GABARAPL2 [
]. It is aslo identified in a unique SNARE complex composed of the Golgi SNAREs GOSR2, STX5 and YKT6 [].
This group of metallopeptidases belong to MEROPS peptidase family M24 (clan MG), subfamily M24A.Methionine aminopeptidase (
) (MAP) catalyses the hydrolytic cleavage of the N-terminal methionine from newly synthesised polypeptides if the penultimate amino acid is small, with different tolerance to Val and Thr at this position [
]. All MAP studied to date are monomeric proteins that require cobalt ions for activity. Two subfamilies of MAP enzymes are known to exist [,
]. While being evolutionary related, they only share a limited amount of sequence similarity, mostly clustered around the residues shown to be involved in cobalt-binding in Escherichia coli MAP []. Subfamily 1 consists of enzymes from prokaryotes as well as eukaryotic MAP-1, while the second group () is made up of archaeal MAP and eukaryotic MAP-2.
The CASH domain is shared by many carbohydrate-binding proteins and sugar hydrolases. The CASH domain is characterised by internal repetitions of glycines and hydrophobic
residues that correspond to the repetitive units of a predicted or observed right-handed β-helix structure of the pectate lyase superfamily. The basic structural unit ofthis family consists of three β-strands that form a single turn of the β-helix. Each turn contains ~20 amino acids, and is normally repeated between 7 and 11 times to
form the elongated helix structure. The repeats show a low degree of sequence identity when compared with each other. The region of homology withthe CASH domain corresponds to the core region of the β-helix, covering from the second to the sixth repeat [
].
Vesicle-associated membrane-protein-associated protein
Type:
Family
Description:
This entry represents a family of vesicle-associated membrane-protein-associated proteins (VAPs) and plant VAP homologs (PVAPs) [
]. VAPs (VAPA and VAPB in humans, VAPA, VAPB and VAPC in other mammals []) are endoplasmic reticulum (ER) proteins that play roles in vesicle trafficking, neurotransmitter release, microtubule organisation, lipid transport and unfolded protein response []. VAP proteins contain an MSP domain in their N-terminal half, which has been shown to interact with proteins containing a FFAT motif, such as members of the oxysterol-binding protein (OSBP) family or the phosphatidylinositol transfer proteins from the PITPNM family []. Yeast VAP homologues are known as Scs2 and Scs22 [].
The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate.PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [
], as well as in archaeal and eukaryotic RNA exosomes [,
], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber [
]. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [,
].This entry represents an RNA-binding domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (
) and PH domain 2 (
), both of which are found in PNPases and exosomes. The core structure of the RNA-binding domain consists of a DNA/RNA-binding 3-helical bundle.
Spindle and kinetochore-associated protein 1 (SKA1) is a component of the SKA1 complex (consists of Ska1, Ska2, and Ska3/Rama1), a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation [
]. It is required for timely anaphase onset during mitosis, when chromosomes undergo bipolar attachment on spindle microtubules leading to silencing of the spindle checkpoint []. The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies. The complex facilitates the processive movement of microspheres along a microtubule in a depolymerisation-coupled manner. SKA1 contains a microtubule-binding domain that interacts with tubulins using multiple contact sites that allow the Ska complex to bind microtubules in multiple modes [].
This is the dimerization domain found in structure-specific recognition protein SSRP1 (POB3 in yeast) and related proteins, which are components of the FACT complex - a general chromatin factor that acts to reorganise nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair [
,
,
,
]. During transcription elongation the FACT complex acts as a histone chaperone that both destabilises and restores nucleosomal structure [,
].This domain has a Pleckstrin homology fold, made of 6 β-strands.
Snf7 family members are small coil-coiled proteins that share protein sequence similarity with budding yeast Snf7, which is part of the ESCRT-III complex that is required for endosome-mediated trafficking via multivesicular body (MVB) formation and sorting [
].Proteins in this entry also includes human CHMPs (charged multivesicular body proteins), budding yeast Did4/Did2,
Arabidopsisvacuolar protein sorting-associated proteins and the archaean
Sulfolobus acidocaldariuscell division protein B which is a component required for cell division, forming polymers with segregating nucleoids [
].
This family includes a 5'-nucleotidase,
, specific for purines (IMP and GMP) [
]. These enzymes are members of the Haloacid Dehalogenase (HAD) superfamily. HAD members are recognised by three short motifs {hhhhDxDx(T/V)}, {hhhh(T/S)}, and either {hhhh(D/E)(D/E)x(3-4)(G/N)} or {hhhh(G/N)(D/E)x(3-4)(D/E)} (where "h"stands for a hydrophobic residue). Crystal structures of many HAD enzymes has verified PSI-PRED predictions of secondary structural elements which show each of the "hhhh"sequences of the motifs as part of beta sheets. This subfamily of enzymes is part of "Subfamily I"of the HAD superfamily by virtue of a "cap"domain in between motifs 1 and 2. This subfamily's cap domain has a different predicted secondary structure than all other known HAD enzymes and thus has been designated "subfamily IG", the domain appears to consist of a mixed alpha/beta fold.
This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (
) which acts as a base excision repair enzyme by severing the glycosylic bond
of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA [].
Superoxide dismutases (SODs) (
) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [
,
,
]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers.The structure of Fe/MnSODs can be divided into two domains, an N-terminal domain with an α-fold and α C-terminal domain with an α/β fold, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist []. The structure of the C-terminal domain is of the α/β type, and consists of a three-stranded antiparallel β-sheet in the order 213, along with four helices in the arrangement α/β2/α/β/α2 [].
Superoxide dismutases (SODs) (
) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [
,
,
]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers.The structure of Fe/MnSODs can be divided into two domains, an N-terminal domain with an α-fold and α C-terminal domain with an α/β fold, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist [
]. The structure of the C-terminal domain is of the α/β type, and consists of a three-stranded antiparallel β-sheet in the order 213, along with four helices in the arrangement α/β2/α/β/α2 [].This entry represents the C-terminal domain of Manganese/iron superoxide dismutase.
Superoxide dismutases (SODs) (
) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [
,
,
]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers.The structure of Fe/MnSODs can be divided into two domains, an N-terminal domain with an α-fold and α C-terminal domain with an α/β fold, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist [
]. The structure of the C-terminal domain is of the α/β type, and consists of a three-stranded antiparallel β-sheet in the order 213, along with four helices in the arrangement α/β2/α/β/α2 [].This entry represents the N-terminal domain of Manganese/iron superoxide dismutase.
TFIIH is a eukaryotic complex composed of two subcomplexes, the CAK (Cdk activating kinase) and the core-TFIIH. This entry represents Tfb1/GTF2H1, a component of the core-TFIIH basal transcription factor, which consists of seven subunits known as XPB, XPD, GTF2H1 (p62), p52, p44, p34, and p8 in humans and Ssl2, Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and Tfb5 in yeast [
]. TFIIH is involved in nucleotide excision repair (NER) of DNA and RNA transcription by RNA polymerase II and I [,
,
].
This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 149 to 199 amino acids in length.
This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 938 amino acids in length. There is a conserved WCF sequence motif and a single completely conserved residue W that may be functionally important.
This superfamily represents the Spen Paralogue and Orthologue C-terminal (SPOC) domain and its structural homologues. This domain has a closed β-barrel fold of complex topology. Proteins that carry a SPOC-like domain include:Spen proteins, such as SHARP (SMRT/HDAC1-associated repressor protein), which carry a SPOC domain at the C-terminal and an RNA-binding motif in the N-terminal; Spen proteins regulate the expression of key transcriptional effectors in diverse signalling pathways, the SHARP protein being a component of transcriptional repression complexes in both nuclear receptor and Notch/RBP-Jkappa signalling pathways [
].The middle domains of Ku70 and Ku80 (which includes the C-terminal α-helical arm and the DNA encircling insertion); the Ku heterodimer, which is composed of Ku70 and Ku80 subunits, contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway [
].
The Ku heterodimer (composed of Ku70
and Ku80
) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C-terminal arm. This alpha helical region embraces the β-barrel domain
of the opposite subunit [
].
The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Ku also binds RNA, mediating the assembly of DNA-PKcs which has a role in ribosomal RNA biogenesis [
]. This domain is found at the C-terminal of Ku which binds to DNA-PKcs [].
The assembly of proteins has been thought to be the sole result of properties inherent in the primary sequence of polypeptides themselves. In some cases, however, structural information from other protein molecules is required for correct folding and subsequent assembly into oligomers [
]. These `helper' molecules are referred to as molecular chaperones, a subfamily of which are the chaperonins []. They are required for normal cell growth (as demonstrated by the fact that no temperature sensitive mutants for the chaperonin genes can be found in the temperature range 20 to 43 degrees centigrade []), and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions []. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10). Type II chaperonins, found in eukaryotic cytosol and in Archaebacteria, comprise only a cpn60 member.The 10kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between 6 to 8 identical subunits, whereas the 60kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits [
]. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner [
,
]. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60.The 60kDa form of chaperonin is the immunodominant antigen of patients with Legionnaire's disease [
], and is thought to play a role in the protection of the Legionella spp. bacteria from oxygen radicals within macrophages. This hypothesis is based on the finding that the cpn60 gene is upregulated in response to hydrogen peroxide, a source of oxygen radicals. Cpn60 has also been found to display strong antigenicity in many bacterial species [], and has the potential for inducing immune protection against unrelated bacterial infections. The RuBisCO subunit binding protein (which has been implicated in the assembly of RuBisCO) and cpn60 have been found to be evolutionary homologues, the RuBisCO subunit binding protein having the C-terminal Gly-Gly-Met repeat found in all bacterial cpn60 sequences. Although the precise function of this repeat is unknown, it is thought to be important as it is also found in 70kDa heat-shock proteins []. The crystal structure of Escherichia coli GroEL has been resolved to 2.8A [].
Proteins in this entry belong to the GPN-loop GTPase family [
], including Npa3 (also known as Gpn1) and Gpn2/3 from budding yeasts. In humans, Npa3 homologue is known as XAB1; Gpn2 is known as GPN2/ATPBD1B; Gpn3 is known as Parcs. Npa3 plays an important part in transporting RNA polymerase II (RNAPII) to the nucleus. The binding of Npa3 with RNAPII is GTP-dependent [
]. Gpn2 and Gpn3 are putative GTPase that have a role in biogenesis of RNA polymerase II and III []. Npa3, Gpn2 and Gpn3 is involved in sister chromatid cohesion [,
].
Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. They are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, fungal, plant and bacterial peroxidases can be viewed as members of a superfamily consisting of 3 major classes. Class I, the intracellular peroxidases, includes yeast cytochrome c peroxidase (CCP), ascorbate peroxidase (AP) and bacterial catalase-peroxidases [
].In chloroplasts of higher plants, oxygen consumption in the absence of electron acceptors is accompanied by production of H2O2 and activated forms of oxygen. Chloroplasts contain several protective systems (such as superoxide dismutase (SOD), alpha-tocopherol and carotenoids), which are effective against various forms of activated oxygen. However, they lack catalase, and the disposal of H2O2 is accomplished by other means.Ascorbic acid is a strong antioxidant that is effective in scavenging superoxide (O2-'), hydroxyl (OH') radicals and singlet oxygen. It can also remove H2O2 in the following reaction:Ascorbate + H2O2 -->dehydroascorbate + 2 H2OAscorbate peroxidase (AP) is the main enzyme responsible for hydrogen peroxide removal in the chloroplasts and cytosol of higher plants.The 3D structure of pea cytosolic ascorbate peroxidase has an overall fold virtually identical to that of CCP [
]. The protein consists of 2 all-alpha domains, between which is embedded the haem group. The most pronounced difference between the AP and CCP structures is the absence of an antiparallel β-hairpin between the G and H helices in the AP molecule.
SMC5 is a core component of the SMC5-SMC6 complex [
,
], a complex involved in repair of DNA double-strand breaks by homologous recombination [,
]. In humans, the SMC5-SMC6 complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks []. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs) []. SMC5 is required for sister chromatid cohesion during prometaphase and mitotic progression; the function seems to be independent of SMC6 [].
The CCAAT-binding factor (CBF, of NFY) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [
,
]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction.The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions [
]. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [,
]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine [].
Members of this family are helicases that catalyse ATP dependent
unwinding of double stranded DNA to single stranded DNA. The familyincludes both Rep and UvrD helicases [
]. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.
This entry represents the catalytic region found in the CAZyme GH116 family members, which presently includes enzymes with beta-glucosidase (), beta-xylosidase (
) , and glucocerebrosidase (
) activity [
]. Proteins containing this domain include animal non-lysosomal glucosylceramidase GBA2, which catalyse the conversion of glucosylceramide to free glucose and ceramide []. GBA2 is involved in sphingomyelin generation and prevention of glycolipid accumulation and may also catalyse the hydrolysis of bile acid 3-O-glucosides, however, the relevance of such activity is unclear in vivo []. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia []. The catalytic nucleophile, identified in is a glutamine-335, with the likely acid/base at Asp-442 and the aspartates at Asp-406 and Asp-458 residues also playing a role in the catalysis of glucosides and xylosides that are beta-bound to hydrophobic groups [
].
Non-lysosomal glucosylceramidase, also known as beta-glucosidase 2 (GBA2) is an enzyme involved in an alternative catabolic pathway of glucosylceramide [
]. GBA2, has been characterised as a bile acid beta-glucosidase []. It is unrelated to other known glucosidases, but it has homologues among bacteria and archaea [].
This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function. It has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [
,
,
]. Examples are:Muramoyl-pentapeptide carboxypeptidase (
)
N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin,
)
Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin,
)
Membrane-bound lytic murein transglycosylase BZinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX [
].Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen [
], stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion [,
], and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism []. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis [].
Aspartate aminotransferase is important for the metabolism of amino acids and Krebs-cycle related
organic acids. In plants, it is involved in nitrogen metabolism and in aspects of carbon and energy metabolism. The enzyme catalyses the reaction:
L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
Aminotransferases share certain mechanistic features with other pyridoxal-phosphate-dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue [
]. This family includes some aromatic-amino-acid aminotransferases too.
Sec6 is a component of the multiprotein exocyst complex. Sec6 interacts with Sec8, Sec10 and Exo70. These exocyst proteins localise to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis-independent manner [
].
This entry represents 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (also known as 3-phosphoshikimate 1-carboxyvinyltransferase), catalyses the sixth step in the biosynthesis from chorismate of the aromatic amino acids (the shikimate pathway) in bacteria (gene aroA), plants and fungi (where it is part of a multifunctional enzyme which catalyses five consecutive steps in this pathway) [
]. The sixth step is the formation of EPSP and inorganic phosphate from shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP).EPSP can use shikimate or shikimate-3-phosphate as a substrate. By binding shikimate, the backbone of the active site is changed, which affects the binding of glyphosate and renders the reaction insensitive to inhibition by glyphosate [
]. On isolation of the discontinuous C-terminal domain, it was found that it binds neither its substrate nor its inhibitor but maintains structural integrity [].Earlier studies suggested that the active site of the enzyme is in the cleft between its two globular domains. When the enzyme binds S3P, there is a conformational change in the isolated N-terminal domain [
]. The sequence of EPSP from various biological sources shows that the structure of the enzyme has been well conserved throughout evolution. Two strongly conserved regions are well defined. The first one corresponds to a region that is part of the active site and which is also important for the resistance to glyphosate []. The second second one is located in the C-terminal part of the protein and contains a conserved lysine which seems to be important for the activity of the enzyme.Since the shikimate pathway is not present in vertebrates but is essential for the life of plants, fungi and bacteria, it is commonly viewed as a target for antimicrobial drug development.
This entry represents the core domain of 3-phosphoshikimate 1-carboxyvinyltransferase and UDP-N-acetylglucosamine 1-carboxyvinyltransferase. These proteins transfer enolpryruvate from phosphoenolpyruvate to 3-phosphoshikimate and UDP-N-acetyl-alpha-D-glucosamine respectively [
,
]. The domain can also be found in the fungal Pentafunctional AROM polypeptide (also known as 3-dehydroquinate synthase), although is this case it does not cover the whole protein but appears in association with other domains such as
. This protein catalyses 5 consecutive enzymatic reactions in prechorismate polyaromatic amino acid biosynthesis [
,
].
3-phosphoshikimate 1-carboxyvinyltransferase, conserved site
Type:
Conserved_site
Description:
This entry represents 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (also known as 3-phosphoshikimate 1-carboxyvinyltransferase), catalyses the sixth step in the biosynthesis from chorismate of the aromatic amino acids (the shikimate pathway) in bacteria (gene aroA), plants and fungi (where it is part of a multifunctional enzyme which catalyses five consecutive steps in this pathway) [
]. The sixth step is the formation of EPSP and inorganic phosphate from shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP).EPSP can use shikimate or shikimate-3-phosphate as a substrate. By binding shikimate, the backbone of the active site is changed, which affects the binding of glyphosate and renders the reaction insensitive to inhibition by glyphosate [
]. On isolation of the discontinuous C-terminal domain, it was found that it binds neither its substrate nor its inhibitor but maintains structural integrity [
].Earlier studies suggested that the active site of the enzyme is in the cleft between its two globular domains. When the enzyme binds S3P, there is a conformational change in the isolated N-terminal domain [
]. The sequence of EPSP from various biological sources shows that the structure of the enzyme has been well conserved throughout evolution and since the shikimate pathway is not present in vertebrates but is essential for the life of plants, fungi and bacteria; it is commonly viewed as a target for weed killers and antimicrobial drug development.This entry represents two conserved regions as signature patterns. The first pattern corresponds to a region that is part of the active site and which is also important for the resistance to glyphosate [
]. The second pattern is located in the C-terminal part of the protein and contains a conserved lysine which seems to be important for the activity of the enzyme.
This entry represents the N-terminal domain found in the CAZyme GH116 family members, which presently includes enzymes with beta-glucosidase (
), beta-xylosidase (
) , and glucocerebrosidase (
) activity [
,
]. The N-terminal is thought to be the luminal domain while the C-terminal is the cytosolic domain.Proteins containing this domain include animal non-lysosomal glucosylceramidase GBA2, which catalyse the conversion of glucosylceramide to free glucose and ceramide [
]. GBA2 is involved in sphingomyelin generation and prevention of glycolipid accumulation and may also catalyse the hydrolysis of bile acid 3-O-glucosides, however, the relevance of such activity is unclear in vivo []. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia [].
This group of serine peptidases belong to MEROPS peptidase family S41 (clan SM), subfamily S41A (C-terminal processing peptidase).
It is a family of C-terminal peptidases with different substrates in different species, including processing of D1 protein of the photosystem II reaction centre in higher plants [], and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in Escherichia coli [].
This entry represents a domain found in the tail-specific proteases, such as retinol-binding protein 3 (also known as IRBP) from animals, C-terminal processing peptidases from algae and tricorn proteases from archaea. This domain share structural similarity with the crotonase fold that is formed from repeated beta/beta/alpha units, which comprises two perpendicular β-sheet surrounded by α-helices. The C-terminal processing peptidases have different substrates in different species, including processing of D1 protein of the photosystem II reaction centre in higher plants [
], and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in Escherichia coli [].The tricorn protease is responsible for degrading oligopeptides, probably derived from the proteasome. Its crystal structure has been resolved to 2 A resolution [].
Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
Type:
Domain
Description:
Aconitase (aconitate hydratase;
) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [,
]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is smaller than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) [].Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [,
]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated [
].IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis [
]. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [
,
]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.3-isopropylmalate dehydratase (or isopropylmalate isomerase;
) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family [
]. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S]cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [
,
]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase , converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis [
]. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast [].This entry represents a region containing 3 domains, each with a 3-layer alpha/beta/alpha topology. This region represents the [4Fe-4S] cluster-binding region found at the N-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the C-terminal of bacterial AcnB. This domain is also found in the large subunit of isopropylmalate dehydratase (LeuC).
Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3
Type:
Homologous_superfamily
Description:
Aconitase (aconitate hydratase;
) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [
,
]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is smaller than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) [].Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [,
]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated [].IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis [
]. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [
,
]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.3-isopropylmalate dehydratase (or isopropylmalate isomerase;
) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family [
]. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S]cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [
,
]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase , converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis [
]. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast [].This superfamily represents a domain with an alpha/beta/alpha topology. This structural domain usually occurs in triplicate, with domains 1 and 3 being the most closely related since they share the same pseudo 2-fold symmetry. This entry represents domains 1 and 3. This triple domain region is found at the N-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the C-terminal of bacterial AcnB; in each case, this region binds the [4Fe-4S]-cluster. This triple domain region is also found in the large subunit of isopropylmalate dehydratase (LeuC).
Aconitase (aconitate hydratase;
) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [
,
]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is smaller than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) [].Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [,
]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated [
].IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis [
]. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [
,
]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.3-isopropylmalate dehydratase (or isopropylmalate isomerase;
) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family [
]. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S]cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [
,
]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase , converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis [
]. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast [].This superfamily represents a domain with an alpha/beta/alpha topology. This structural domain usually occurs in triplicate, with domains 1 and 3 being the most closely related since they share the same pseudo 2-fold symmetry. This entry represents domain 2. This triple domain region is found at the N-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the C-terminal of bacterial AcnB; in each case, this region binds the [4Fe-4S]-cluster.
This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.b. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion interactions [
,
].
This entry represents the N terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. Glyoxal oxidase catalyses the oxidation of aldehydes to carboxylic acids, coupled with reduction of dioxygen to hydrogen peroxide. It is an essential component of the extracellular lignin degradation pathways of the wood-rot fungus Phanerochaete chrysosporium [
].
E or 'early' set domains are associated with the catalytic domain of galactose oxidase at the C-terminal end. Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates, and possesses a unique mononuclear copper site essential for catalyzing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active centre necessary for the reaction was found to be situated at a tyrosine residue. The C-terminal domain of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end, and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others [,
,
,
,
].
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [
,
,
]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) [
].This entry represents EF-Ts (EF1B) proteins found primarily in bacteria, mitochondria and chloroplasts.
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [
,
,
]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) [
].This entry represents the C-terminal dimerisation domain found primarily in EF-Tu (EF1A) proteins from bacteria, mitochondria and chloroplasts.
This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2), MmaA1-4 (methoxymycolic acid synthase A1-4) and tuberculostearic acid methyltransferase UfaA1. All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases [
]. This entry also includes S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis, which is a methyltransferase that modifies short-chain fatty acids [].Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase)
catalyses the reaction:
S-adenosyl-L-methionine + phospholipid olefinic fatty acid ->S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.
The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [
].
Glyoxalase I (lactoylglutathione lyase) catalyzes the first step
of the glyoxal pathway in the following reaction:glutathione + methylglyoxal = (R)-S-lactoylglutathione
S-lactoylglutathione is then converted by glyoxalase II to lactic acid [
].Glyoxalase I is a ubiquitous enzyme which binds one mole of zinc
per subunit. The bacterial and yeast enzymes are monomeric while the mammalianone is homodimeric.
The sequence of glyoxalase I is well conserved. In bacteria and mammals theenzyme is a protein of about 130 to 180 residues while in fungi it is about
twice as long. In these organisms the enzyme is built out of the tandem repeatof a homologous domain.
Caleosins are a family of lipid-associated proteins that are ubiquitous in plants and true fungi. In plants, caleosinss are Ca(2+)-binding oil-body surface proteins [
]. Later, caleosin was identified as a putative peroxygenase, which is involved in oxylipin metabolism during biotic and abiotic stress responses in Arabidopsis []. The calcium binding domain is probably related to the calcium-binding EF-hands motif .
The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition [
]. TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. Trs120 is a subunit specific to the TRAPP II complex [] along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way []. It is likely that there is a complex function for TRAPP II in multiple pathways [].
This entry contains a number of protein families with apparently unrelated functions. The yeast YAP binding proteins are stress response and redox homeostasis proteins, induced by hydrogen peroxide or induced in response to alkylating agent methyl methanesulphonate (MMS) [
,
]. Aberrant root formation protein 4 (ALF4) of Arabidopsis thaliana (Mouse-ear cress),is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation []. Glomulin (FAP68) is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12 [,
].
This entry represents the C-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with DUF3475 (
).
PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth [
].
This entry represents the N-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with DUF668 (
).
PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth [
].
A conserved motif was identified in the LOC118487 protein was called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2]domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation [
]. Eukaryotic NADH-ubiquinone oxidoreductase 19kDa (NDUFA8) subunit []. The CHCH domain was previously called DUF657 [].
Cyclophilins exhibit peptidyl-prolyl cis-trans isomerase (PPIase) activity (
), accelerating protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides [
,
]. They also have protein chaperone-like functions [] and are the major high-affinity binding proteins for the immunosuppressive drug cyclosporin A (CSA) in vertebrates [].Cyclophilins are found in all prokaryotes and eukaryotes, and have been structurally conserved throughout evolution, implying their importance in cellular function [
]. They share a common 109 amino acid cyclophilin-like domain (CLD) and additional domains unique to each member of the family. The CLD domain contains the PPIase activity, while the unique domains are important for selection of protein substrates and subcellular compartmentalisation [].This entry represents the cyclophilin peptidyl-prolyl cis-trans isomerase family. The family includes RING-type E3 ubiquitin-protein ligase PPIL2, which is thought to be an inactive PPIase [].
In yeast the high-affinity transporter for external inorganic phosphate is not essential since a constitutive, low-affinity transporter exists. The induction of the yeast protein is depressed by phosphate starvation.
This entry represents the small nuclear ribonucleoprotein Sm D2 (Smd2) [
]. Smd2 is a component of the SM core complex, a ring complex consists of six or seven subunits []. SM complex associates with the snRNPs and is involved in the RNA-processing pathways []. Small nuclear ribonucleoproteins (snRNPs) U1, U2, U4/U6 and U5 snRNPs play important roles in pre-mRNA splicing. The U1, U2, U4 and U5 small nuclear RNAs (snRNAs) present in these particles, each contains a conserved single-stranded sequence element, the Sm binding site. The Sm binding site interacts with the Sm proteins to form an Sm core structure [
].
This entry represents the C-terminal domain of DNAB-like helicases. DnaB helicase unwinds the DNA duplex at the Escherichia coli chromosome replication fork. The mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, however, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis [
,
,
].
NDUFAF7 (NADH:ubiquinone oxidoreductase complex assembly factor 7), also known as MidA or mitochondrial protein midA homologue, plays a role in mitochondrial complex I activity [
].
Analysis of the Brix (biogenesis of ribosomes in Xenopus) protein leaded to the identification of a region of 150-180 residues length, called the Brix
domain, which is found in six protein families: one archaean family (I) including hypothetical proteins (one per genome); and five eukaryote families, each named according to a representative member and including close homologues of this prototype: (II) Peter Pan (D. melanogaster) and SSF1/2 (S.cerevisiae); (III) RPF1 (S. cerevisiae); (IV) IMP4 (S. cerevisiae); (V) Brix (X.laevis) and BRX1 (S. cerevisiae); and (VI) RPF2 (S.cerevisiae).Typically, a protein sequence belonging to the Brix domain superfamily contains a highly charged N-terminal segment (about 50 residues) followed by a single copy of the Brix domain and another highly charged C-terminal region (about 100 residues). The archaean sequences have two unique characteristics: (1) the charged regions are totally absent at the N terminus and are reduced in number to about 10 residues at the C terminus; and (2) the C-terminal part of the Brix domain itself is minimal. Two eukaryote groups have large insertions within the C-terminal region: about 70 residues in the group III and about 120 in the group II. Biological data for some proteins in this family suggest a role in ribosome biogenesis and rRNA binding [
,
,
,
].
The YTH (YT521-B homology) domain has been suggested to be an evolutionarily conserved m6A-dependent RNA binding domain [
]. Proteins containing this domain includes mammalian YTHD and YTDC proteins, Arabidopsis CPSF30 (At1g30460), budding yeast Pho92 and fission yeast Mmi1. In Saccharomyces cerevisiae, Pho92 is a post-transcriptional regulator that regulates Pho4 mRNA stability by binding to the 3'-UTR in a phosphate-dependent manner. Its YTH domain exhibits RNA-binding activity [
]. In Schizosaccharomyces pombe, Mmi1 has been identified as eliminating meiosis-specific mRNAs []. Rat YTHDC1 (also known as YT521-B) is an alternative splicing regulator that recognises and binds N6-methyladenosine (m6A)-containing RNAs. The YTH domain of YT521-B is a RNA-binding domain with a very degenerate sequence-specificity [
].
Synonym: UDP-galactose 4-epimerase UDP-glucose 4-epimerase (
)
interconverts UDP-glucose and UDP-galactose which are precursors of glucose- andgalactose-containing exopolysaccharides (EPS) [
]. Arabidopsis thaliana has five genes encoding functional UDP-D-glucose/UDP-D-galactose 4-epimerase [].A set of related proteins, some
of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are not included in this family.
This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex [
].Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer [
]. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This family of large subunit ribosomal proteins is called the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain [
]. L7 and L12 are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises L7/L12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that L7/L12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors [
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
].In eukaryotes, the proteins that perform the equivalent function to L7/L12 are called P1 and P2, which do not share sequence similarity with L7/L12. However, a bacterial L7/L12 homologue is found in some eukaryotes, in mitochondria and chloroplasts [
]. In archaea, the protein equivalent to L7/L12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to L7/L12 [].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain [
]. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.
Cytidine deaminase (
) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (
) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [
,
]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion.Such a region is also found in other proteins [
,
]:Yeast cytosine deaminase (
) (gene FCY1) which transforms cytosine into uracil.
Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA.Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate.Bacillus cereus blasticidin-S deaminase (
), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S.
Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA.B. subtilis hypothetical protein yaaJ.Escherichia coli hypothetical protein yfhC.Yeast hypothetical protein YJL035c.
This entry represents a group of lysine methyltransferases. Characterised members of this family are protein methyltransferases targetting Lys residues in specific proteins, including calmodulin, VCP, Kin17 and Hsp70 proteins [
,
,
,
].
Glyoxalase I (lactoylglutathione lyase) catalyzes the first step
of the glyoxal pathway in the following reaction:glutathione + methylglyoxal = (R)-S-lactoylglutathione
S-lactoylglutathione is then converted by glyoxalase II to lactic acid [
].Glyoxalase I is a ubiquitous enzyme which binds one mole of zinc
per subunit. The bacterial and yeast enzymes are monomeric while the mammalianone is homodimeric.
The sequence of glyoxalase I is well conserved. In bacteria and mammals theenzyme is a protein of about 130 to 180 residues while in fungi it is about
twice as long. In these organisms the enzyme is built out of the tandem repeatof a homologous domain.
The Drosophila protein 'enhancer of rudimentary' (gene (e(r)) is a small protein of 104 residues whose function is not yet clear. From an evolutionary point of view, it is highly conserved [
] and has been found to exist in probably all multicellular eukaryotic organisms. ERH has been implicated in the regulation of pyrimidine biosynthesis, DNA replication, transcription, mRNA splicing, cellular proliferation, tumorigenesis, and the Notch signaling pathway []. Fission yeast homologue of ERH is implicated in meiotic mRNA elimination during vegetative growth. It forms a stoichiometric complex with Mmi1 to promote meiotic mRNA decay and facultative heterochromatin assembly [,
,
] in which the formation of ERH dimer is essential for the complex function.ERH has been shown to interact with SAFB1/SAFB2 (scaffold attachment factor-B 1/2) at the nuclear matrix to regulate SR protein phosphorylation [
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This entry represents the ribosomal protein L18 from bacteria and chloroplasts. The archaebacterial type is not included in this family.
Copper/Zinc superoxide dismutase (SODC) [
,
,
] is one of the three forms of an enzyme that catalyzes the dismutation of superoxide radicals. SODC binds one atom each of zinc and copper. Various forms of SODC are known: a cytoplasmic form in eukaryotes, an additional chloroplast form in plants, an extracellular form in some eukaryotes, and a periplasmic form in prokaryotes. The metal binding sites are conserved in all the known SODC sequences []. This entry contains 2 patterns, the first contains the two histidine residues that bind the copper atom; the second one is located in the C-terminal section of SODC and contains a cysteine which is involved in a disulphide bond.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].Ribosomal protein L9 is one of the proteins from the large ribosomal subunit.
In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongsto a family of ribosomal proteins grouped on the basis of sequence similarities [
].The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker [
]. Each domain contains an rRNA binding site, and the protein functions as astructural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an α-helix and a three-stranded mixed
parallel, anti-parallel β-sheet packed against the central α-helix. The long central α-helix is exposed to solvent in the middle and participates in thehydrophobic cores of the two domains at both ends.
This entry represents ribosomal L9 proteins found in bacteria and plastids, but not in mitochondria.
This entry represents proteins SOSEKI 1-5 (SOK1-5) from Arabidopsis thaliana. SOSEKI proteins (SOK1-5) integrate apical-basal and radial organismal axes to localize to polar cell edges and contain a DIX oligomerization domain that resembles that in the animal Dishevelled polarity regulator [
,
]. SOK2 is also known as Protein UPSTREAM OF FLC (UFC, At5g10150) and is part of a three-gene cluster containing FLC, UFC and DFC, which is coordinately regulated in response to vernalization [,
].
DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (
), the other NAD (
), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [
,
].Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [,
]. This domain is found in many but not all ATP-dependent DNA ligase enzymes (
). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (
), and in Saccharomyces cerevisiae (Baker's yeast) (
), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (
) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation [
].
DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (
), the other NAD (
), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [
,
].Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [
,
].
DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (
), the other NAD (
), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [
,
].Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [
,
]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (
) and NAD-dependent DNA ligase (
) [
].
DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (
), the other NAD (
), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [
,
].Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [
,
]. This region is found in many but not all ATP-dependent DNA ligase enzymes (
). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase [
].
This entry represents U4/U6.U5 tri-snRNP-associated proteins, including SART1 from animals, Snu66 from yeasts and DOT2 from Arabidopsis. SART1 and its yeast homologue, Snu66, are part of the U4/U6.U5 snRNP complex involved in pre-mRNA splicing via spliceosome [
,
,
]. DOT2 plays a role in root, shoot and flower development [,
].
These proteins exhibit homology to the Saccharomyces cerevisiae Mtq2 (also know as PrmC [
]). Mtq2 methylates eRF1 on 'Gln-182' using S-adenosyl L-methionine as methyl donor. eRF1 needs to be complexed to eRF3 in its GTP-bound form to be efficiently methylated [,
,
]. In bacteria, the methylation of RF1/RF2 by PrmC is important for normal growth, to increase the affinity of RF1/RF2 for ribosomes and to enhance translation termination [,
].Human homologue of Mtq2 is called hemK methyltransferase family member 2 (HEMK2, also known as N6AMT1), which is an N6-adenine-specific DNA methyltransferase [
].
The first characterised member of the Kae1/TsaD family was annotated as Gcp for O-sialoglycoprotein endopeptidase [
], but this activity could not be confirmed []. Later, its homologue, Kae1 from Pyrococcus abyssi, has been shown to have DNA-binding properties and apurinic-endonuclease activity []. Members of this family have since been studied in yeast, archaea and bacteria resulting in sometimes conflicting data, several proposed functions and annotations but no definitive characterisation. For instance, some members have been linked to DNA maintenance in bacteria and mitochondria [] and transcription regulation and telomere homeostasis in eukaryotes [,
], but their function remained unclear. Recent research indicates that this family is involved in the biosynthesis of N6-threonylcarbamoyl adenosine, a universal modification found at position 37 of tRNAs that read codons beginning with adenine [,
].
This domain was identified in proteins including Kae1 and Gcp (YgjD), which were originally thought to be endopeptidases belonging to the peptidase M22 family [
]. However, there is a lack of experimental evidence to support peptidase activity as a general property, and this has not been confirmed in other orthologues [,
]. Recent research indicates that the Kae1 and Gcp proteins are involved in the biosynthesis of N6-threonylcarbamoyl adenosine, a universal modification found at position 37 of tRNAs that read codons beginning with adenine []. This domain is also present in Bacillus subtilis YdiC and Escherichia coli YeaZ. These proteins have been recently renamed as TsaB, and have also been shown to be involved in N6-Threonylcarbamoylad enonsine (t(6)A) biosynthesis [,
].
This entry represents the TsaD protein family that is widely distributed. TsaD and its archaeal homologue Kae1 (
) belong to the Kae1/TsaD family (
), a conserved protein family with unknown function.
This entry includes bacterial TsaD and its homologues, such as Qri7 (localize to the mitochondria) from budding yeast
[]. TsaD (also known as Gcp or YgjD) was originally described as a glycoprotease essential for cell viability [
] and a critical mediator involved in the modification of cell wall peptidoglycan synthesis and/or cell division []. Gcp is a member of the Kae1/TsaD family, required for the formation of a threonylcarbamoyl group on adenosine at position 37 in tRNAs that read codons beginning with adenine []. YgjD has been renamed as TsaD, and it has been shown that YgjD and proteins YrdC (TsaC), YjeE (TsaE), and YeaZ (TsaB), are necessary and sufficient for t6A biosynthesis in vitro, and may constitute a complex [].The first characterised member of the Kae1/TsaD family was annotated as Gcp for O-sialoglycoprotein endopeptidase [
], but this activity could not be confirmed []. Later, its homologue, Kae1 from Pyrococcus abyssi, has been shown to have DNA-binding properties and apurinic-endonuclease activity []. Members of this family have since been studied in yeast, archaea and bacteria resulting in sometimes conflicting data, several proposed functions and annotations but no definitive characterisation. For instance, some members have been linked to DNA maintenance in bacteria and mitochondria [] and transcription regulation and telomere homeostasis in eukaryotes [,
], but their function remained unclear. Recent research indicates that this family is involved in the biosynthesis of N6-threonylcarbamoyl adenosine, a universal modification found at position 37 of tRNAs that read codons beginning with adenine [,
].
This family represents Ycf20, it is found in cyanobacteria and is also encoded in plant and algal chloroplasts; its function is unknown. As the family is exclusively found in phototrophic organisms it may therefore play a role in photosynthesis.
This entry represents the eukaryotic Vacuolar protein sorting-associated protein 41 (Vps41), a subunit of the homotypic vacuole fusion and vacuole protein sorting (HOPS) complex, which is essential for membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of protein transport [
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]. This protein interacts with Caspase-8, which plays a key role in apoptosis and development []. In humans, Vps41 variants prevent the formation of a functional HOPS complex, causing disorders such as dystonia associated with lysosomal abnormalities and neurodegenerative diseases [
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].
