EF2 (or EFG) participates in the elongation phase of protein synthesis by promoting the GTP-dependent translocation of the peptidyl tRNA of the nascent protein chain from the A-site (acceptor site) to the P-site (peptidyl tRNA site) of the ribosome. EF2 also has a role after the termination phase of translation, where, together with the ribosomal recycling factor, it facilitates the release of tRNA and mRNA from the ribosome, and the splitting of the ribosome into two subunits [
]. EF2 is folded into five domains, with domains I and II forming the N-terminal block, domains IV and V forming the C-terminal block, and domain III providing the covalently-linked flexible connection between the two. Domains III and V have the same fold (although they are not completely superimposable and domain III lacks some of the superfamily characteristics), consisting of an alpha/beta sandwich with an antiparallel β-sheet in a (beta/alpha/beta)x2 topology []. This double split beta/alpha/beta fold is also seen in a number of ribonucleotide binding proteins. It is the most common motif occurring in the translation system and is referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif. This entry represents domain III of EF2 proteins.
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 EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [
,
]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome.EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, facilitates the movement of peptidyl-tRNA from the A to the P site, being critical for the structural transition to take place [
].Included in this entry is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins that is homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA [
,
,
,
,
,
,
,
,
].
The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [
], including regulation of transcription by RNA polymerase II [,
]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Hfi1 (known as Transcriptional adapter 1, Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes.
In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate (
): fumaratereductase (Frd) is used in anaerobic growth, and succinate dehydrogenase (Sdh)
is used in aerobic growth. Both complexes consist of two main components: amembrane-extrinsic component composed of a FAD-binding flavoprotein and an
iron-sulphur protein; and an hydrophobic component composed of a membraneanchor protein and/or a cytochrome B.
In eukaryotes mitochondrial succinate dehydrogenase (ubiquinone) (
)
is an enzyme composed of two subunits: a FAD flavoprotein and and iron-sulphurprotein.
The flavoprotein subunit is a protein of about 60 to 70 Kd to which FAD is
covalently bound to a histidine residue which is located in the N-terminalsection of the protein [
]. The sequence around that histidine is well conserved in Frd and Sdh from various bacterial and eukaryotic species [].The terms succinate dehydrogenase and fumarate reductase may be used interchangeably in certain systems. However, a number of species have distinct complexes, with the fumarate reductase active under anaerobic conditions. This model represents the fumarate reductase flavoprotein subunit from several such species in which a distinct succinate dehydrogenase is also found.
This family represents the eukaryotic targeting protein for Xklp2 (TPX2). TPX2 is a microtubule-associated protein that targets a plus end-directed motor (Xklp2) to the minus ends of microtubules in the mitotic spindle. In Xenopus, it has been shown that Xklp2 protein is required for centrosome separation and maintenance of spindle bi-polarity [
]. It is phosphorylated during mitosis in a microtubule-dependent way []. TPX2 activates Aurora A kinase by promoting its autophosphorylation and protects the phosphorylated residue against dephosphorylation [].
This entry represents the central domain found in the eukaryotic targeting protein for Xklp2 (TPX2) protein. TPX2 is a microtubule-associated protein that targets a plus end-directed motor (Xklp2) to the minus ends of microtubules in the mitotic spindle. This domain is close to the C-terminal of TPX2. The protein importin alpha regulates the activity of TPX2 by binding to the nuclear localisation signal in this domain [
].
Superoxide dismutases (SODs) are ubiquitous metalloproteins that prevent damage by oxygen-mediated free radicals by catalysing the dismutation of superoxide into molecular oxygen and hydrogen peroxide [
]. Superoxide is a normal by-product of aerobic respiration and is produced by a number of reactions, including oxidative phosphorylation and photosynthesis. The dismutase enzymes have a very high catalytic efficiency due to the attraction of superoxide to the ions bound at the active site [,
].There are three forms of superoxide dismutase, depending on the metal cofactor: Cu/Zn (which binds both copper and zinc), Fe and Mn types. The Fe and Mn forms are similar in their primary, secondary and tertiary structures, but are distinct from the Cu/Zn form [
]. Prokaryotes and protists contain Mn, Fe or both types, while most eukaryotic organisms utilise the Cu/Zn type.Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structural analysis supports the notion of independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [
,
,
,
,
,
,
,
].
Superoxide dismutases (SODs) are ubiquitous metalloproteins that prevent damage by oxygen-mediated free radicals by catalysing the dismutation of superoxide into molecular oxygen and hydrogen peroxide [
]. Superoxide is a normal by-product of aerobic respiration and is produced by a number of reactions, including oxidative phosphorylation and photosynthesis. The dismutase enzymes have a very high catalytic efficiency due to the attraction of superoxide to the ions bound at the active site [,
].There are three forms of superoxide dismutase, depending on the metal cofactor: Cu/Zn (which binds both copper and zinc), Fe and Mn types. The Fe and Mn forms are similar in their primary, secondary and tertiary structures, but are distinct from the Cu/Zn form [
]. Prokaryotes and protists contain Mn, Fe or both types, while most eukaryotic organisms utilise the Cu/Zn type.This entry represents the superoxide dismutase proteins as well as a related family of copper chaperones for superoxide dismutases. These cytosolic proteins deliver copper to Cu/Zn superoxide dismutases and are vital to their function [
].
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.Glycosyltransferase family 43
comprises enzymes with only one known activity: beta-glucuronyltransferase(GlcAT-I;
) [
].GlcAT-I is a key enzyme involved in the initial steps of proteoglycan synthesis [
]. GlcAT-I catalyzes the transfer of a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region of trisaccharide Gal-beta-(1-3)-Gal-beta-(1-4)-Xyl of proteoglycans. The enzyme has two subdomains that bind the donor and acceptor substrate separately []. The active site is located at the cleft between both subdomains in which the trisaccharide molecule is oriented perpendicular to the UDP [].
RER1 family proteins are involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi
compartment. The C terminus of yeast Rer1p interacts with a coatomer complex [].
Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [
], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E.Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus [
].This is the C-terminal domain of cyclins.
Clp is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin [
] and is a member of peptidase family S14. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP [,
], although the P subunit alone does possess some catalytic activity []. This entry represents the P subunit.Proteases highly similar to ClpP have been found to be encoded in the genome
of bacteria, metazoa, some viruses and in the chloroplast of plants, but seems to be absent in archaea, mollicutes and some fungi []. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium [
]. Active site consists of the triad Ser, His and Asp []; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function [,
].
Clp protease proteolytic subunit /Translocation-enhancing protein TepA
Type:
Family
Description:
This entry includes peptidases from the MEROPS peptidase family S14, including ClpP endopeptidase and translocation-enhancing protein TepA.ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin [
]. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence ofATP [
], although the P subunit alone does possess some catalytic activity. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity. Translocation-enhancing protein TepA displays sequence similarity to ClpP. It is required for efficient translocation of pre-proteins across the membrane [
].
PI31 is a regulatory subunit of the immunoproteasome which is an inhibitor of the 20S proteasome in vitro. PI31 is also an Fbxo7.Skp1 binding partner. Fbxo7 is an F-box protein, which are the substrate-recognition components of the Skp1-Cul1-F box protein (SCF) E3 ubiquitin ligases. The interaction between PI31 and Fbxo7.Skp1 occurs via the beta sheets of a N-terminal domain present in both proteins and known as FP(Fbxo7/PI31) domain. The structure of PI31 FP domain contains a novel alpha/β-fold and two intermolecular contact surfaces [
].This entry represents the N-terminal domain of the PI31 proteasome regulator.
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [
,
].In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit [
].In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory.The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal β-barrel, a central domain containing the nucleotide-binding site and a C-terminal α bundle domain of 7 and 6 helices, respectively, in the alpha and beta subunits [
]. This entry represents the C-terminal domain of the alpha subunit.
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.This entry represents a domain that is found in the C terminus of the F1 ATP synthase beta subunit and in the C terminus of the V-ATPase alpha and beta subunits.
MORF4 (mortality factor on chromosome 4), MRG15 (MORF4-related gene on chromosome 15) and MRGX (MORF4-related gene on chromosome X) are members of the MRG protein family that were first identified as transcription factors involved in cellular senescence. All expressed members of the MRG family are localized to the nucleus and have predicted motifs that indicate they function as chromatin remodeling complex components. MORF4, MRG15 and MRGX share a common C-terminal part but a different N-terminal part. The C-terminal similarity of all MRG family members (MORF4, MRG15 and MRGX homologues) defines a new conserved protein domain. The ~170 amino acid MRG domain binds a plethora of transcriptional regulators and chromatin-remodeling factors, including the histone deacetylase transcriptional corepressor mSin3A and the nuclear protein PAM14 (protein-associated MRG, 14kDa) [
,
].The MRG domain consists of three conserved blocks. It is predominantly hydrophobic, and consists of mainly α-helices that are arranged in a three layer sandwich topology. The hydrophobic core is stabilised by interactions among a number of conserved hydrophobic residues. The molecular surface is largely hydrophobic, but contains a few hydrophilic patches [
,
,
].
This entry represents MRG protein family, whose members include MORF4L1/2 (MRG15/MRGX) and MSL3L1/2 from humans, ESA1-associated factor 3 (Eaf3) from yeasts and male-specific lethal 3 (MSL3) from flies. They contain an N-terminal chromodomain that binds H3K36me3, a histone mark associated with transcription elongation [
]. Saccharomyces cerevisiae Eaf3 is a component of both NuA4 histone acetyltransferase and Rpd3S histone deacetylase complexes [
,
]. It was found that Eaf3 mediates preferential deacetylation of coding regions through an interaction between the Eaf3 chromodomain and methylated H3-K36 that presumably results in preferential association of the Rpd3 complex []. The Drosophila MSL proteins (MSL1, MSL2, MSL3, MLE, and MOF) are essential for elevating transcription of the single X chromosome in the male (X chromosome dosage compensation) [
]. Together with two partlyredundant non-coding RNAs, roX1 and roX2, they form the MSL complex, also known as dosage compensation complex or DCC. MSL complex upregulates transcription by spreading the histone H4 Lys16 (H4K16) acetyl mark [
] and allows compensation for the loss of one X-chromosomal allele by increasing the transcription from the retained allele []. The MSL3 chromodomain has been shown to bind DNA and methylated H4K20 in vitro []. Human MORF4L1, also known as MRG15, is a component of the NuA4 histone acetyltransferase complex that transcriptional activates genes by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. NuA4 complex may also play a direct role in DNA repair when directly recruited to sites of DNA damage. MRG15 is also a component of the mSin3A/Pf1/HDAC complex which acts to repress transcription by deacetylation of nucleosomal histones. MRG15 was found to interact with PALB2, a tumour suppressor protein that plays a crucial role in DNA damage repair by homologous recombination [
]. Furthermore, MRG15 play a role in the response to double strand breaks (DSBs) by recruiting the BRCA complex (BRCA1, PALB2, BRCA2 and RAD51) to sites of damaged DNA [,
].
This entry includes various FAD dependent oxidoreductases: glycerol-3-phosphate dehydrogenase (
), sarcosine oxidase beta subunit (
), D-amino acid dehydrogenase (
), D-aspartate oxidase (
).
D-amino acid oxidase (
) (DAMOX or DAO) is an FAD flavoenzyme that catalyzes the oxidation of neutral and basic D-amino acids into their corresponding keto acids. DAOs have been characterised and sequenced in fungi and vertebrates where they are known to be located in the peroxisomes. D-aspartate oxidase (
) (DASOX) [
] is an enzyme, structurally related to DAO, which catalyzes the same reaction but is active only toward dicarboxylic D-amino acids. In DAO, a conserved histidine has been shown [
] to be important for the enzyme's catalytic activity.
The whirly family members are plant transcription factors that bind to single-stranded DNA and regulate defense gene expression [
,
,
]. They may contribute to plastid genome stability by protecting against illegitimate repeat-mediated recombination [,
].
This superfamily represents a ssDNA-binding transcriptional regulator domain consisting of a helix-swapped dimer of beta(4)-alpha motifs. This domain is found as a C-terminal domain in the transcriptional co-activator PC4 (also known as P15; where it is a dimer of two separate motifs), and in the plant transcriptional regulator PBF-2 (where it is a single chain domain formed by a tandem repeat of two motifs).Transcriptional regulators play a critical role in controlling the level of transcription from specific genes in response to different stimuli. Members of this family of transcriptional regulators, which preferentially bind single-stranded DNA, include PBF-2 from plants, the mammalian nuclear factor 1-X (NF1-X), and positive cofactor 4 (PC4). These proteins are structurally similar, consisting of a helix-swapped dimer of beta(4)-alpha motifs.The plant defence transcription factor PBF-2 is comprised of four p24 subunits that interact through a helix-loop-helix motif to produce a central pore [
]. PBF-2 functions as part of the plant's defence system in response to the detection of a pathogen. Upon stimulation, PBF-2 induces several signal transduction pathways leading to changes in the expression of defence genes, including the pathogenesis-related (PR) genes.NF1-X is one of several NF1 proteins that function as transcription factors. NF1-X consists of two functionally distinct domains: a conserved N-terminal DNA-binding domain and a C-terminal transcriptional regulatory domain. NF1-X binds to the promoter for the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase gene [
].PC4 (or P15) possess the ability to co-activate and suppress transcription via its DNA-binding activity. PC4 has been shown to stimulate transcription
in vitrowith diverse activators, including VP16, thyroid hormone receptor, BRCA-1, often involving TFIIA. PC4 and TFIIA are thought to facilitate the assembly of the pre-initiation complex. The repressive activity of PC4 can be alleviated by the transcription factor TFIIH, which protects promoters from PC4 repression [
]. PC4 consists of two domains: an N-terminal regulatory domain and a C-terminal cryptic DNA-binding domain. The protein acts as a dimer with two ssDNA binding channels running in opposite directions to each other [].
Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of tRNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 () from Saccharomyces cerevisiae (Baker's yeast) acts on pre-tRNA-Phe, while Dus 2 (
) acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD [
]. Some family members may be targeted to the mitochondria and even have a role in mitochondria []. The signature pattern used in this entry contains a conserved cysteine which could be one of the active site residues.
Dihydrouridine synthases (Dus) is a large family of flavoenzymes comprising eight subfamilies. They catalyse the NADPH-dependent synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. Mainly, they contain two functional conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition. However, DUS2 is distinguished from its paralogues and its fungi orthologues by the acquisition of an additional domain, a double stranded RNA binding domain (dsRBD), which serves as the main tRNA binding module [
,
]. Dus 1 (
) from Saccharomyces cerevisiae (Baker's yeast) acts on pre-tRNA-Phe, while Dus 2 (
) acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD [
]. Some family members may be targeted to the mitochondria and even have a role in mitochondria []. DUS3 (not included in this entry) contains an extra zinc finger N-terminal to the Dus domain.
The maspardin protein (Mast syndrome, spastic paraplegia, autosomal recessive with dementia) is a member of the AB hydrolase superfamily that has been shown to localise to intracellular endosomal/trans-Golgi transportation vesicles and may function in protein transport and sorting [
]. The protein has also been shown to interact with CD4, and may play a role as a negative regulatory factor in CD4-dependent T-cell activation []. Although sequence alignments show maspardin to be a member of the AB hydrolase superfamily, they also show it to lack the nucleophile-acid-histidine triad required for catalytic function, suggesting that maspardin is unlikely to function as an enzyme []. Defects in the maspardin gene are the cause of spastic paraplegia autosomal recessive type 21 (SPG21), also known as Mast syndrome. Mast syndrome is a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs [].
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 contains 30S ribosomal protein S15P/S13e and 40S ribosomal protein S13, which belong to the S15P family.
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 domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [
].
Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds
to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteinswhich, on the basis of sequence similarities [
,], groups bacterial and plant chloroplast S15;archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi
and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.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 [
,
].
The RNA-binding domains of the ribosomal protein S15 and the influenza virus non-structural protein NS1 share the same structural fold, consisting of three helices in an irregular array. S15 is one of 21 proteins in the small, bacterial 30S ribosomal subunit, and is required for assembly of the subunit through its binding to 16S rRNA [
]. The multifunctional glutamyl-prolyl-tRNA synthase (EPRS) contains three tandem repeats linking two catalytic domains, all three of which contribute to RNA-binding; the second repeated element bears structural resemblance to the S15/NS1 RNA-binding domain [].
The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [
].
The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [
].
This entry represents a homeobox transcription factor KN domain conserved from
fungi to human and plants []. Genes encoding these proteins were first identified as TALE homeobox proteins in eukaryotes, (including KNOX and MEIS genes) [,
,
]. They have been classified [,
,
].
Homeobox genes, which encode homeodomain (HD) transcription
factors, are known to be key regulators of both plant and animal development.In plants homeobox genes are divided into several groups by sequences, one of
which is the KNOX (for knotted1-type homeobox) family. Proteins of this familyshare other conserved domains, the KNOX domain and ELK domain, which is
immediately upstream of the HD. The ELK domain spans ~21 amino acids and wasdubbed for a highly conserved series of Glu, Leu, and Lys amino acids. It
could function as a nuclear localization signal. The ELK domain also isconsidered to act as a protein-protein interaction domain, but the precise
role of this domain has not been determined [,
,
,
].The ELK domain contains repeating hydrophobic residues and has been predicted
to form an amphipathic helix [].
This domain is found in a family of proteins have been implicated in chlorophyll degradation [
,
]. Intriguingly members of this family are also found in non-photosynthetic bacteria.
Subtilases [
] are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.This entry represents the conserved sequence around the aspartic acid (Asp) active site.
These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues 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. The peptidases in this group of sequences include:Insulinase, insulin-degrading enzyme (
)
Mitochondrial processing peptidase alpha subunit, (Alpha-MPP,
)
Pitrlysin, Protease III precursor (
)
Nardilysin, (
)
Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (
)
Coenzyme PQQ synthesis protein F (
)
These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [
] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].
This entry represents domains with a two-layer α/β structure found in metalloenzymes such as LuxS (S-ribosylhomocysteinase;
) and metallopeptidases belonging to MEROPS peptidase family M16. These domains share the same active site motif of HxxEH located in the first core helix, but differ in one of the metal-binding residues. LuxS, the AI-2 (autoinducer-2) producing enzyme for quorum sensing in bacteria, is a homodimeric iron-dependent metalloenzyme containing two identical tetrahedral metal-binding sites similar to those found in peptidases and amidases, although it contains an extra N-terminal strand [
,
]. Some M16 family metallopeptidases, such as mitochondrial processing peptidase (MPP), share the same common fold elaborated with many extra additional structures []. These peptidases usually contain a duplication of this domain, although only the N-terminal domain binds the catalytic metal.Domains found in metallopeptidases and non-peptidase homologues belonging to MEROPS peptidase family M16 (clan ME), subfamilies M16A, M16B and M16C; include:Insulinase, insulin-degrading enzyme (
)
Mitochondrial processing peptidase alpha subunit, (Alpha-MPP,
)
Pitrlysin, Protease III precursor (
)
Nardilysin, (
)
Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (
)
Coenzyme PQQ synthesis protein F (
)
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role.
Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [].A number of proteases dependent on divalent cations for their activity have
been shown [,
] to belong to one family, on the basis of sequence similarity.These enzymes are listed below:
Insulinase (
) (also known as insulysin or insulin-degrading enzyme or IDE), a cytoplasmic enzyme which seems to be involved in the
cellular processing of insulin, glucagon and other small polypeptides.Escherichia coli protease III (
) (pitrilysin) (gene ptr), a
periplasmic enzyme that degrades small peptides.Mitochondrial processing peptidase (
) (MPP). This enzyme
removes the transit peptide from the precursor form of proteins importedfrom the cytoplasm across the mitochondrial inner membrane. It is composed
of two non-identical homologous subunits termed alpha and beta. The betasubunit seems to be catalytically active while the alpha subunit has
probably lost its activity.Nardilysin (
) (N-arginine dibasic convertase or NRD convertase)
this mammalian enzyme cleaves peptide substrates on the N terminus of Argresidues in dibasic stretches.
Klebsiella pneumoniae protein pqqF. This protein is required for the
biosynthesis of the coenzyme pyrrolo-quinoline-quinone (PQQ). It is thoughtto be protease that cleaves peptide bonds in a small peptide (gene pqqA)
thus providing the glutamate and tyrosine residues necessary for thesynthesis of PQQ.Saccharomyces cerevisiae (Baker's yeast) protein AXL1, which is involved in axial budding [
].Eimeria bovis sporozoite developmental protein.E. coli hypothetical protein yddC and HI1368, the corresponding
Haemophilus influenzae protein.Bacillus subtilis hypothetical protein ymxG.Caenorhabditis elegans hypothetical proteins C28F5.4 and F56D2.1.It should be noted that in addition to the above enzymes, this family also
includes the core proteins I and II of the mitochondrial bc1 complex (alsocalled cytochrome c reductase or complex III), but the situation as to the
activity or lack of activity of these subunits is quite complex:In mammals and yeast, core proteins I and II lack enzymatic activity.In Neurospora crassa and in potato core protein I is equivalent to the beta
subunit of MPP.In Euglena gracilis, core protein I seems to be active, while subunit II is
inactive.These proteins do not share many regions of sequence similarity; the most
noticeable is in the N-terminal section. This region includes a conservedhistidine followed, two residues later by a glutamate and another histidine.
In pitrilysin, it has been shown [,
] that this H-x-x-E-H motif is involved inenzyme activity; the two histidines bind zinc and the glutamate is necessary
for catalytic activity. Non-active members of this family have lost from oneto three of these active site residues. This signature pattern only detects active members of the M16 peptidase family.
This entry represents an N-terminal domain found in metallopeptidases and non-peptidase homologues belonging to MEROPS peptidase family M16 (clan ME), subfamilies M16A, M16B and M16C. Members of this family include:Insulinase, insulin-degrading enzyme (
)
Mitochondrial processing peptidase alpha subunit, (Alpha-MPP,
)
Pitrlysin, Protease III precursor (
)
Nardilysin, (
)
Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (
)
Coenzyme PQQ synthesis protein F (
)
These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [
] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity.The proteins classified as non-peptidase homologues 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.
This entry represents lysine-tRNA ligase class II.Lysine-tRNA synthesis is catalysed by two unrelated families of tRNA ligases: class-I or class-II. In eubacteria and eukaryota lysine-tRNA ligases belong to class II, the same family as aspartyl tRNA ligase. The lysine-tRNA ligase class Ic family is present in archaea and some eubacteria [
]. Moreover in some eubacteria there is a gene X, which is similar to a part of lysine-tRNA ligase from class II.Lysine-tRNA ligase is duplicated in some species with, for example in Escherichia coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots"of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [
].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].
The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed β-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids [
]. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See ). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule
. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [
,
]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.
The lysosomal degradation of several sphingolipids requires the presence of four small glycoproteins called saposins, generated by proteolytic processing of a common precursor, prosaposin [
]. Saposins have three conserved disulphide bridges, and display a 5-helical, closed, folded leaf topology. Other proteins have been shown to have structures that closely resemble saposin, such as the antimicrobial peptides NK-lysin and granulysin [,
]. Some proteins contain saposin-like domains, such as prophytepsin, an acid protease from plants, and J3-crystallin, an eye-lens protein from jellyfish, both of which contain circularly permuted saposin motifs called swaposin [,
]. In some saposins and saposin-like domains, lipid-binding can promote conformational changes and oligomerization.
Peptidase family A1, also known as the pepsin family, contains peptidases with bilobed structures [
,
]. The two domains most probably evolved from the duplication of an ancestral gene encoding a primordial domain []. The active site is formed from an aspartic acid residue from each domain. Each aspartic acid occurs within a motif with the sequence D(T/S)G(T/S). Exceptionally, in the histoaspactic peptidase from Plasmodium falciparum, one of the Asp residues is replaced by His [
]. A third essential residue, Tyr or Phe, is found on the N-terminal domain only in a β-hairpin loop known as the "flap"; this residue is important for substrate binding, and most members of the family have a preference for a hydrophobic residue in the S1 substrate binding pocket. Most members of the family are active at acidic pH, but renin is unusually active at neutral pH. Family A1 peptidases are found predominantly in eukaryotes (but examples are known from bacteria [
,
]). Currently known eukaryotic aspartyl peptidases and homologues include the following:Vertebrate gastric pepsins A (
), gastricsin (
, also known pepsin C), chymosin (
; formerly known as rennin), and cathepsin E (
). Pepsin A is widely used in protein sequencing because of its limited and predictable specificity. Chymosin is used to clot milk for cheese making.
Lysosomal cathepsin D (
).
Renin (
) which functions in control of blood pressure by generating angiotensin I from angiotensinogen in the plasma.
Memapsins 1 (
; also known as BACE 2) and 2 (
; also known as BACE) are membrane-bound and are able to perform one of the two cleavages (the beta-cleavage, hence they are also known as beta-secretases) in the beta-amyloid precursor to release the the amyloid-beta peptide, which accumulates in the plaques of Alzheimer's disease patients.
Fungal peptidases such as aspergillopepsin A (
), candidapepsin (
), mucorpepsin (
; also known as
Mucorrennin), endothiapepsin (
), polyporopepsin (
), and rhizopuspepsin (
) are secreted for sapprophytic protein digestion.
Fungal saccharopepsin (
) (proteinase A) (gene PEP4) is implicated in post-translational regulation of vacuolar hydrolases.
Yeast barrierpepsin (
) (gene BAR1); a protease that cleaves alpha-factor and thus acts as an antagonist of the mating pheromone.
Fission yeast Sxa1 may be involved in degrading or processing the mating pheromones [
].In plants, phytepsin (
) degrades seed storage proteins and nepenthesin (EC 3.4.23.12) from a pitcher plant digests insect proteins. Also are included Aspartic proteinase 36 and Aspartic proteinase 39, which contribute to pollen and ovule development and have an important role in plant development in Arabidopsis [
].Plasmepsins (
and
) from Plasmodium species are important for the degradation of host haemoglobin.
Non-peptidase homologues where one or more active site residues have been replaced, include mammalian pregnancy-associated glycoproteins, an allergen from a cockroach, and a xylanase inhibitor [
].
Saposins are small lysosomal proteins that serve as activators of various
lysosomal lipid-degrading enzymes []. They probably act by isolating thelipid substrate from the membrane surroundings, thus making it more
accessible to the soluble degradative enzymes. All mammalian saposinsare synthesized as a single precursor molecule (prosaposin) which contains
four Saposin-B domains, yielding the active saposins after proteolyticcleavage, and two Saposin-A domains that are removed in the activation
reaction. The Saposin-B domains also occur in other
proteins, many of them active in the lysis of membranes [,
].
Hydroxymethylglutaryl-coenzyme A synthase, N-terminal
Type:
Domain
Description:
Hydroxymethylglutaryl-CoA synthase (
) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA [
].HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria [
]. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [,
].This entry represents the N-terminal domain of HMG-CoA synthase enzymes from both eukaryotes and prokaryotes.
Hydroxymethylglutaryl-CoA synthase (
) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA [
].HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria [
]. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [,
].This entry is specific for eukaryotic HMG-CoA synthase enzymes.
Hydroxymethylglutaryl-coenzyme A synthase, active site
Type:
Active_site
Description:
Hydroxymethylglutaryl-CoA synthase (
) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA [
].HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria [
]. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [,
].This entry represents the sequence surrounding the catalytic cysteine required for nucleophilic attack in the first step of the reaction, the acetylation of the enzyme by acetyl-CoA.
Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain
Type:
Domain
Description:
Hydroxymethylglutaryl-CoA synthase (
) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA [
].HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria [
]. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [,
].This entry represents the C-terminal domain of HMG-CoA synthase enzymes from both eukaryotes and prokaryotes.
dTDP-4-dehydrorhamnose reductase (
) catalyses the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose, which is the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose [
]. dTDP-rhamnose is essential for growth of mycobacteria []. dTDP-L-rhamnose is the precursor of L-Rhamnose (L-Rha), a component of the lipopolysaccharide (LPS) core and several O antigen polysaccharides of Pseudomonas [].Methionine adenosyltransferase 2 subunit beta (MAT2B) also belongs to this family. It is the regulatory subunit of MAT2A, an enzyme that catalyses the formation of S-adenosylmethionine (AdoMet) from methionine and ATP [
]. Also in this family is the probable dTDP-4,6-dihydroxy-2-methyloxan-3-one 4-ketoreductase (oleU) from Streptomyces antibioticus, which is required for the biosynthesis of the aglycone antibiotic oleandomycin [
].
GPCR family 3 receptors (also known as family C) are structurally similar to other GPCRs, but do not show any significant sequence similarity and thus represent a distinct group. Structurally they are composed of four elements; an N-terminal signal sequence; a large hydrophilic extracellular agonist-binding region containing several conserved cysteine residues which could be involved in disulphide bonds; a shorter region containing seven transmembrane domains; and a C-terminal cytoplasmic domain of variable length [
]. Family 3 members include the metabotropic glutamate receptors, the extracellular calcium-sensing receptors, the gamma-amino-butyric acid (GABA) type B receptors, and the vomeronasal type-2 receptors [,
,
,
]. As these receptors regulate many important physiological processes they are potentially promising targets for drug development.GABA is the principal inhibitory neurotransmitter in the brain, and signals through ionotropic (type A and type C) and metabotropic (type B) receptor systems. The type B receptors have been cloned, and photoaffinity labelling experiments suggest that they correspond to two highly conserved receptor forms in the vertebrate nervous system [
]. These receptors are involved in the fine tuning of inhibitory synaptic transmission []. Presynaptic receptors inhibit neurotransmitter release by down-regulating high-voltage activated calcium channels, while postsynaptic receptors decrease neuronal excitability by activating a prominent inwardly rectifying potassium (Kir) conductance that underlies the late inhibitory postsynaptic potentials [,
]. The type B receptors negatively couple to adenylyl cyclase and show sequence similarity to the metabotropic receptors for the excitatory neurotransmitter L-glutamate. The physiological form of the B receptor is a heterodimer of the B1 and B2 subtypes, in which B1 seems to bind agonists, while B2 mediates coupling to G proteins [,
,
].Metabotropic glutamate receptor-like proteins (Grl) are similar in structure to GABA-B receptors and belong to the same receptor family [
,
].
This group represents an ionotropic glutamate-like receptor, plant type. They have sequence similarity with animal ionotropic glutamate receptor [
,
]. Interestingly, despite sharing a common structure, GLRs and iGluRs display major sequence divergences, especially in key domains such as the receptor, the pore, and the 'gate'. Electrophysiological characterization of PpGLR1, AtGLR3.2, and AtGLR3.3 showed their ligand-independent activity, providing evidence for functional differences between iGluRs and at least these specific GLRs []. Animal ionotropic glutamate receptors (iGluRs) functions in the nervous system. while plant glutamate receptor-like (GLR) homologues are involved in many plant-specific physiological functions, such as sperm signaling in moss, pollen tube growth, root meristem proliferation, innate immune and wound responses [].
Many eukaryotic proteins are anchored to the cell surface via glycosylphosphatidylinositol (GPI), which is posttranslationally attached to the C terminus by GPI transamidase. The mammalian GPI transamidase is a complex of at least four subunits, GPI8, GAA1, PIG-S, and PIG-T. PIG-U is thought to represent a fifth subunit in this complex and may be involved in the recognition of either the GPI attachment signal or the lipid portion of GPI [
].
The ureohydrolase superfamily includes arginase (
), agmatinase (
), formimidoylglutamase (also known as formiminoglutamase;
) and proclavaminate amidinohydrolase (
) [
]. These enzymes share a 3-layer α-β-alpha structure [,
,
], and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways. Arginase, which catalyses the conversion of arginine to urea and ornithine,
is one of the five members of the urea cycle enzymes that convert ammoniato urea as the principal product of nitrogen excretion [
]. There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia.Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals. Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide.Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics [
].This entry represents the 3-layer α-β-alpha domain which characterises the ureohydrolase superfamily.
The ureohydrolase superfamily includes arginase (
), agmatinase (
), formiminoglutamase (
) and proclavaminate amidinohydrolase (
) [
]. These enzymes share a 3-layer α-β-alpha structure [,
,
], and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways. Arginase, which catalyses the conversion of arginine to urea and ornithine,
is one of the five members of the urea cycle enzymes that convert ammoniato urea as the principal product of nitrogen excretion [
]. There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia.Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals. Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide.Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics [
].Three conserved regions that contain charged residues which are involved in the binding of the two manganese ions in the active site are located in loop segments of the central β-sheet [
,
,
,
]. The signature pattern of this entry contains two aspartate residues that are involved in manganese binding.
The ureohydrolase superfamily includes arginase (
), agmatinase (
), formiminoglutamase (
) and proclavaminate amidinohydrolase (
) [
]. These enzymes show trimeric or hexameric structures and share a 3-layer α-β-alpha structure [,
,
,
], playing important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways.Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion []. There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia.Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals. Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide.Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics [
].
Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. PP2 is translocated in the assimilate stream where its lectin activity or RNA-binding properties can exert effects over long distances. PP2-like genes have been identified in many plant species, indicating a wide distribution of PP2 genes in the plant kingdom [
].This entry represents PP2 and PP2-like proteins.
The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue [
]. The structure of MBOAT has been revealed [].This family includes Diacylglycerol O-acyltransferase 1 (DGAT1) and Lysophospholipid acyltransferase 7 (MBOAT7) from humans. DGAT1 catalyzes the terminal and only committed step in triacylglycerol synthesis by using diacylglycerol and fatty acyl CoA as substrates [
]. It also functions as the major acyl-CoA retinol acyltransferase (ARAT) in the skin, where it acts to maintain retinoid homeostasis and prevent retinoid toxicity leading to skin and hair disorders []. MBOAT7 participates in the regulation of triglyceride metabolism through the phosphatidylinositol acyl-chain remodeling regulation [].
BAG domains are present in Bcl-2-associated athanogene 1 and silencer of death domains. The BAG proteins are modulators of chaperone activity, they bind to HSP70/HSC70 proteins and promote substrate release. The proteins have anti-apoptotic activity and increase the anti-cell death function of BCL-2 induced by various stimuli. BAG-1 binds to the serine/threonine kinase Raf-1 or Hsc70/Hsp70 in a mutually exclusive interaction. BAG-1 promotes cell growth by binding to and stimulating Raf-1 activity. The binding of Hsp70 to BAG-1 diminishes Raf-1 signalling and inhibits subsequent events, such as DNA synthesis, as well as arrests the cell cycle. BAG-1 has been suggested to function as a molecular switch that encourages cells to proliferate in normal conditions but become quiescent under a stressful environment [
,
].BAG-family proteins contain a single BAG domain, except for human BAG-5 which has four BAG repeats [
]. The BAG domain is a conserved region located at the C terminus of the BAG-family proteins that binds the ATPase domain of Hsc70/Hsp70. The BAG domain is evolutionarily conserved, and BAG domain containing proteins have been described and/or proven in a variety of organisms including Mus musculus (Mouse), Xenopus spp., Drosophila spp., Bombyx mori (Silk moth), Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast), Schizosaccharomyces pombe (Fission yeast), and Arabidopsis thaliana (Mouse-ear cress).The BAG domain has 110-124 amino acids and is comprised of three anti-parallel α-helices, each approximately 30-40 amino acids in length. The first and second helices interact with the serine/threonine kinase Raf-1 and the second and third helices are the sites of the BAG domain interaction with the ATPase domain of Hsc70/Hsp70. Binding of the BAG domain to the ATPase domain is mediated by both electrostatic and hydrophobic interactions in BAG-1 and is energy requiring.
Phosphatidylinositol-glycan biosynthesis class T protein (PIG-T, also known as Gpi16 in budding yeasts) is a component of the glycosylphosphatidylinositol (GPI) trans-amidase complex that adds GPIs to newly synthesized proteins [
]. Mammalian GPI transamidase consists of at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and PIG-U, all five of which are required for its function. It is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a tightly associated core that is only weakly associated with PIG-U. The exact function of PIG-S is unclear [].
The helicase/SANT-associated (HSA) domain is found in eukaryotic proteins, including Helicase SRCAP/p400/DOM [
], Probable global transcription activator SNF2L2/brahma-homologue and Chromatin modification-related protein EAF1 []. While each family has the core sequences that define the HSA domain, they each also have additional sequences that distinguish these families from one another. For example, the sequence HWDY(L/C)EEEM(Q/V) is found in the SRCAP/p400/DOM family, whereas the sequence HQE(Y/F)LNSILQ is found in the SNF2 /brahma family [].HSA was initially predicted to be a DNA-binding domain [
], but it was later reported to be responsible for the binding to nuclear actin-related proteins (ARPs) and actin []. In addition to the SANT and helicase domains, the HSA domain is also found in association with the bromo domain [].
The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain [
]. This domain is also found on other proteins linked to the ubiquitin-proteasome system.
Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [
]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [].This entry represents the C-terminal subdomain 2 from several tetrapyrrole methylases, which consist of two non-similar domains. These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:Uroporphyrinogen III methyltransferase (
) (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [
].Precorrin-2 C20-methyltransferase CobI/CbiL (
), which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [
]. In some species, this enzyme is part of a bifunctional protein.Precorrin-4 C11-methyltransferase CobM/CbiF (
), which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [
].Sirohaem synthase CysG (
), domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [
].Diphthine synthase (
), which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.
O-Glycosyl hydrolases (
) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [
,
]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.Glycoside hydrolase family 43
includes enzymes with the following activities, beta-xylosidase (
), alpha-L-arabinofuranosidase (
); arabinanase (
), and xylanase (
).
This entry represents the DNA-binding domain of the E2F and DP proteins, which have a fold related to the winged-helix DNA-binding motif [
]. The mammalian transcription factor E2F plays an important role in regulating theexpression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [
].
The E2F family of transcription factors plays a crucial role in the control of cell cycle [
,
] and action of tumour suppressor proteins. This family consists of eight members and is divided into activators (E2F1-3) and repressors (E2F4-8) depending on cellular context, target gene and cofactors []. The E2F proteins contain several evolutionarily conserved domains found in most members of the family. These domains include a DNA-binding domain, a dimerisation domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumour suppressor protein association domain which is embedded within the transactivation domain []. Classical E2Fs (E2F1-6) contain one DNA-binding domain which form heterodimers with DP proteins; atypical family members, E2F7 and E2F8, possess two DNA-binding domains, form homodimers or heterodimers, thus regulating transcription in a DP-independent manner [].
Alpha-N-acetylglucosaminidase is a lysosomal enzyme required for the stepwise degradation of heparan sulphate [
]. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations [].
Alpha-N-acetylglucosaminidase is a lysosomal enzyme required for the stepwise degradation of heparan sulphate [
]. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB, or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This C-terminal domain has an all alpha helical fold [].
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.This family represents subunits called delta in bacterial and chloroplast ATPase, or OSCP (oligomycin sensitivity conferral protein) in mitochondrial ATPase (note that in mitochondria there is a different delta subunit,
). The OSCP/delta subunit appears to be part of the peripheral stalk that holds the F1 complex alpha3beta3 catalytic core stationary against the torque of the rotating central stalk, and links subunit A of the F0 complex with the F1 complex. In mitochondria, the peripheral stalk consists of OSCP, as well as F0 components F6, B and D. In bacteria and chloroplasts the peripheral stalks have different subunit compositions: delta and two copies of F0 component B (bacteria), or delta and F0 components B and B' (chloroplasts) [
,
].
F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily
Type:
Homologous_superfamily
Description:
F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.The subunits called delta in bacterial and chloroplast ATPase, or OSCP (oligomycin sensitivity conferral protein) in mitochondrial ATPase (note that in mitochondria there is a different delta subunit,
). The OSCP/delta subunit appears to be part of the peripheral stalk that holds the F1 complex alpha3beta3 catalytic core stationary against the torque of the rotating central stalk, and links subunit A of the F0 complex with the F1 complex. In mitochondria, the peripheral stalk consists of OSCP, as well as F0 components F6, B and D. In bacteria and chloroplasts the peripheral stalks have different subunit compositions: delta and two copies of F0 component B (bacteria), or delta and F0 components B and B' (chloroplasts) [
,
].This superfamily represents the N-terminal six α-helix bundle domain of the OSCP/delta subunit [
].
ATP synthase (proton-translocating ATPase) [
,
] is a componentof the cytoplasmic membrane of eubacteria, the inner membrane of mitochondria,
and the thylakoid membrane of chloroplasts. The ATPase complex is composed ofan oligomeric transmembrane sector, called CF(0), which acts as a proton
channel, and a catalytic core, termed coupling factor CF(1).One of the subunits of the ATPase complex, known as subunit delta in bacteria
and chloroplasts, or the Oligomycin Sensitivity Conferral Protein (OSCP) inmitochondria, seems to be part of the stalk that links CF(0) to CF(1). It
either transmits conformational changes from CF(0) into CF(1) or is involvedin proton conduction [
].The different delta/OSCP subunits are proteins of approximately 200 amino-acid
residues - once the transit peptide has been removed in the chloroplast andmitochondrial forms - which show only moderate sequence homology.This entry represents a conserved site in the C-terminal section of these proteins.
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
Type:
Domain
Description:
A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be
specific for the D-isomer of their substrate have been shown to be functionally and structurally related. All contain a glycine-rich region located in the central section of these enzymes, this region corresponds to the NAD-binding domain. This domain is inserted into the catalytic domain. The catalytic domain is described in ().
This domain is a NAD/FAD-binding fold found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [
,
,
]. Ubiquitin-activating enzyme (E1 enzyme) [
,
] activates ubiquitin by firstadenylating with ATP its C-terminal glycine residue and thereafter linking
this residue to the side chain of a cysteine residue in E1, yielding anubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is
transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2).
Cytidine deaminase (
) (cytidine aminohydrolase) catalyses the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate
deaminase () (dCMP deaminase) hydrolyses dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [
,
]. The deaminases possess either one or two conserved zinc-coordinating (Z) motifs, with the consensus amino acid signature H-x(1)-E-x(24,28)-P-C-x(2,4)-C. This motif is required for catalytic activity. Zinc coordination is mediated by a histidine and two cysteines []. The CMP/dCMP-type deaminase domain consists ofa central β-sheet with one or more α-helices on each side [
].This entry represents the CMP/dCMP-type deaminase domain. Some enzymes, such as riboflavin biosynthesis protein PYRR, have a non-functional deaminase domain that lacks the catalytically essential zinc-binding residues [
].
This superfamily represents a structural domain with a core fold consisting of α-β(2)-(α-β)2 that folds into three layers (alpha/beta/alpha); some members may contain an extra C-terminal strand. This domain is found in several types of proteins, including:Cytidine deaminase (
), including both mono-domain enzymes [
] and two-domain enzymes that arose through a duplication and which contain extra helices in the N-terminal domain [].Deoxycytidylate (dCMP) deaminase (
) [
].Guranine deaminase GuaD (
) [
].Cytosine deaminase (
) [
].AICAR transformylase domain (
) of the bifunctional purine biosynthesis enzyme ATIC; this protein consists of two domains of this fold with extra secondary structures within and in between the two core motifs [
].Hypothetical protein TM1506 from Thermotoga maritima also contains a domain of this structure.
Deoxycytidylate deaminase (
) (dCMP deaminase) hydrolyzes deoxycytidylate mono phosphate (dCMP) into deoxyuridine mono phosphate (dUMP), thus providing the nucleotide substrate for thymidylate synthase. The enzyme requires zinc for catalytic activity which is regulated by the ratio of dCTP to dTTP, both the end products of the pyrimidine salvage pathway [
,
,
]. It contains a cytidine and deoxycytidylate deaminase domain. This entry also includes CDADC1 (cytidine and dCMP deaminase domain-containing protein 1), also known as testis development protein NYD-SP15, which may play an important role in testicular development and spermatogenesis [
]. CDADC1 contains two cytidine and deoxycytidylate deaminase domains.
This domain can be found in IRX15/IRX15L/IGXM from plants and in protein PBDC1 from animals and fungi. IRX15/IRX15L and IGXM play a role in xylan biosynthesis in plant cell walls. However, they have different functions [
]. The function of IRX15/IRX15L is not clear. GXM1/GXM2/GXM3 are methyltransferases catalysing 4-O-methylation of GlcA side chains on xylan [,
].The function of PBDC1 (polysaccharide biosynthesis domain-containing protein) is not clear.
This entry includes IRREGULAR XYLEM IRX15/IRX15L and GLUCURONOXYLAN METHYLTRANSFERASE1 (GXM1), GXM2 and GXM3 from plants. GXMs and IRX15/15L are all expressed in secondary wall-forming cells and they are all involved in xylan biosynthesis. However, they may have different functions [
]. GXM1/GXM2/GXM3 are methyltransferases catalysing 4-O-methylation of GlcA side chains on xylan [,
]. The function of IRX15/IRX15L is not clear.
NADH dehydrogenase ubiquinone Fe-S protein 4 mitochondrial-like
Type:
Family
Description:
This entry includes NADH dehydrogenase [ubiquinone] iron-sulfur protein 4 (NDUS4), an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), initially identified in Neurospora crassa as a 21kDa protein [,
]. It is believed that members of this family are not involved in catalysis. This entry also includes uncharacterised bacterial sequences.
Histone proteins have central roles in both chromatin organisation (as
structural units of the nucleosome) and gene regulation (as dynamic componentsthat have a direct impact on DNA transcription and replication). Eukaryotic
DNA wraps around a histone octamer to form a nucleosome, the first order ofcompaction of eukaryotic chromatin. The core histone octamer is composed of a
central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the corehistone contains a common structural motif, called the histone fold, which
facilitates the interactions between the individual core histones.In addition to the core histones, there is a "linker histone"called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures.
Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [,
]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA.The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15
domain is also characterised by high sequence homology among the family oflinker histones. The highly conserved H15 domain is essential for the binding
of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III),with a β-hairpin at the C terminus. There is also a short three-residue
stretch between helices I and II that is in the β-strand conformation.Together with the C-terminal β-hairpin, this strand forms the third strand
of an antiparallel β-sheet [,
,
,
].Proteins known to contain a H15 domain are:
- Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are
simultaneously present in a single cell. For example, the nucleatederythrocytes of birds contain both H1 and H5, the latter being an extreme
variant of H1.- Eukaryotic MHYST family of histone acetyltransferase. Histone
acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon-amino group of lysine within the basic NH2-termini of histones, which bind
the acidic phosphates of DNA [].This entry represents the H15 domain.
Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [
,
]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity [].Crystallographic analysis of various small G proteins revealed the presence of a 20kDa catalytic domain that is unique for the whole superfamily [
,
]. The domain is built of five alpha helices (A1-A5), six β-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg2 and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg2 binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base [].The small GTPase superfamily can be divided into at least 8 different families, including:Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus.Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export.Rab small GTPases. GTP-binding proteins involved in vesicular traffic.Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation.Ras small GTPases. GTP-binding proteins involved in signalling pathways.Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking.Roc small GTPases domain. Small GTPase domain always found associated with the COR domain.The SAR1 [
,
] protein, first identified in budding yeast, is a 21kDa GTP-binding protein involved in vesicular transport between the endoplasmic
reticulum and the Golgi []. It is a GTP-binding protein that takes part in theformation of secretory vesicles by binding to an ER type II membrane
protein, Sec12p []. It is evolutionary conserved and seems to be presentin all eukaryotes.
SAR1 is generally included in the RAS 'superfamily' of small GTP-binding
proteins, but it is only slightly related to other RAS proteins. It alsodiffers from RAS proteins in that it lacks cysteine residues at the C terminus
and is therefore not subject to prenylation. SAR1 is slightly related to ARFs.
Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [
,
]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity [].Crystallographic analysis of various small G proteins revealed the presence of a 20kDa catalytic domain that is unique for the whole superfamily [
,
]. The domain is built of five alpha helices (A1-A5), six β-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg2 and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg2 binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base [].The small GTPase superfamily can be divided into at least 8 different families, including:Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus.Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export.Rab small GTPases. GTP-binding proteins involved in vesicular traffic.Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation.Ras small GTPases. GTP-binding proteins involved in signalling pathways.Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking.Roc small GTPases domain. Small GTPase domain always found associated with the COR domain.This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), and Arp
(Arf-related proteins). Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound
Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.
Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [
,
]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity [].Crystallographic analysis of various small G proteins revealed the presence of a 20kDa catalytic domain that is unique for the whole superfamily [
,
]. The domain is built of five alpha helices (A1-A5), six β-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg2 and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg2 binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base [].The small GTPase superfamily can be divided into at least 8 different families, including:Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus.Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export.Rab small GTPases. GTP-binding proteins involved in vesicular traffic.Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation.Ras small GTPases. GTP-binding proteins involved in signalling pathways.Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking.Roc small GTPases domain. Small GTPase domain always found associated with the COR domain.This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp
(Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other.
The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound
Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.
This domain is found in F-box and other domain-containing plant proteins. Its precise function is unknown, but it is thought to be associated with nuclear processes [
]. In fact, several family members are annotated as being similar to transcription factors.
This is a family of integral membrane proteins containing transmembrane helices. This family used to be known as DUF81.The TauE proteins are involved in the transport of anions across the cytoplasmic membrane [
,
] during taurine metabolism as an exporter of sulfoacetate [].
This entry represents the uridine kinase like proteins. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyses the following reaction:ATP + Uridine = ADP + UMP
A cDNA for uridine kinase from mouse brain was found which encodes a protein of 277 amino acids. A truncated form of the cDNA was expressed in Escherichia coli, and shown to display uridine
kinase activity and to readily form a tetramer, the most active form of the wild-type enzyme. Sequence analysis has identified three ATP-binding site consensus motifs. The predicted secondary structure, and sequence comparison with kinases of known structure, is consistent with uridine kinase having the alpha/beta core nucleotide-binding fold common to many kinases [].
This entry represents a family of uridine kinase proteins [
].Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyses the following reaction:ATP + Uridine = ADP + UMP
A cDNA for uridine kinase from mouse brain was found which encodes a protein of 277 amino acids. A truncated form of the cDNA was expressed in Escherichia coli, and shown to display uridine
kinase activity and to readily form a tetramer, the most active form of the wild-type enzyme. Sequence analysis has identified three ATP-binding site consensus motifs. The predicted secondary structure, and sequence comparison with kinases of known structure, is consistent with uridine kinase having the alpha/beta core nucleotide-binding fold common to many kinases [].
Phosphoribulokinase (PRK)
catalyses the ATP-dependent phosphorylation of
ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms [
]. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while
those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible
oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine
salvage pathway. It catalyzes the following reaction:ATP + Uridine = ADP + UMP
Pantothenate kinase (
) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP.
The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function and it is necessary for retrograde trafficking in the Golgi apparatus and for protein glycosylation [
,
].
This entry represents the N-terminal domain of subunit 2 of the COG complex. The COG complex comprises eight proteins COG1-8 and plays critical roles in Golgi structure and function and it is involved in retrograde vesicular trafficking within the Golgi apparatus. [
,
,
]. COG complex,together with exocyst, Golgi-associated retrograde protein (GARP) and Dsl1 complexes, is a member of the CATHR (complexes associated with tethering containing helical rods) family sharing an evolutionary origin and structural features [].
The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function. It is necessary for retrograde trafficking in the Golgi apparatus and for protein glycosylation [
,
]. COG complex, together with exocyst, Golgi-associated retrograde protein (GARP) and Dsl1 complexes, is a member of the CATHR (complexes associated with tethering containing helical rods) family sharing an evolutionary origin and structural features []. This domain is found in the C-terminal of COG complex subunit 2 proteins and consists of a conserved α-helical bundle. In Arabidopsis, COG2 forms a complex with FPP3/VETH1 and FPP2/VETH2 and ensures the correct secondary cell wall (SCW) deposition pattern by recruiting exocyst components to cortical microtubules in xylem cells during secondary cell wall deposition [
].
FHA and SMAD (MH2) domains share a common structure consisting of a sandwich of eleven β-strands in two sheets with Greek key topology. Forkhead-associated (FHA) domains were originally identified as a sequence profile of about 75 amino acids, whereas the full-length domain is closer to about 150 amino acids. FHA domains are found in transcription factors, kinesin motors, and in a variety of other signalling molecules in organisms ranging from eubacteria to humans. FHA domains are protein-protein interaction domains that are specific for phosphoproteins. FHA-containing proteins function in maintaining cell-cycle checkpoints, DNA repair and transcriptional regulation. FHA domain proteins include the Chk2/Rad53/Cds1 family of proteins that contain one or more FHA domains, as well as a Ser/Thr kinase domain [
,
,
]. SMAD (Mothers against decapentaplegic (MAD) homologue) domain proteins are found in a range of species from nematodes to humans. These highly conserved proteins contain an N-terminal MH1 domain that contacts DNA, and is separated by a short linker region from the C-terminal MH2 domain, the later showing a striking similarity to FHA domains. SMAD proteins mediate signalling by the TGF-beta/activin/BMP-2/4 cytokines from receptor Ser/Thr protein kinases at the cell surface to the nucleus. SMAD proteins fall into three functional classes: the receptor-regulated SMADs (R-SMADs), including SMAD1, -2, -3, -5, and -8, each of which is involved in a ligand-specific signalling pathway []; the comediator SMADs (co-SMADs), including SMAD4, which interact with R-SMADs to participate in signalling []; and the inhibitory SMADs (I-SMADs), including SMAD6 and -7, which block the activation of R-SMADs and Co-SMADs, thereby negatively regulating signalling pathways []. Domains with this fold are also found as the transactivation domain of interferon regulatory factor 3 (IRF3), which has a weak homology to SMAD domains [
], and the N-terminal domain of EssC protein in Staphylococcus aureus.
The forkhead-associated (FHA) domain [
] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded β-sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.
