Histone H2A is a small, highly conserved nuclear protein that, together with two molecules each of histones H2B, H3 and H4, forms the eukaryotic nucleosome core [
]; the nucleosome octamer winds ~146 DNA base-pairs. In the mouse, histone H2A can be replaced by histone H2A-like 1 [].
The nearly ubiquitous polyamines (putrescine, spermidine and spermine) are
polycationic mediators of cell proliferation and differentiation whosefunctions likely provide both stability and neutralisation for nucleic acids.
The following polyamine biosynthetic enzymes are evolutionary related []:Spermidine synthase (
) (putrescine aminopropyltransferase). It
catalyzes the last step in the biosynthesis of spermidine from arginine andmethionine; the conversion of putrescine to spermidine using decarboxylated
S-adenosylmethionine as the cofactor.Spermine synthase (
) (spermidine aminopropyltransferase). It
converts spermidine into spermine using decarboxylated S-adenosylmethionineas the cofactor.
Putrescine N-methyltransferase (
). It catalyzes a step in the
biosynthesis of nicotine in plants; the methylation of putrescine to N-methylputrescine using S-adenosylmethionine as the cofactor.
The Thermotoga maritima spermidine synthase monomer consists of two domains:an N-terminal domain composed of six β-strands, and a Rossmann-like C-
terminal domain. The larger C-terminal catalytic core domainconsists of a seven-stranded β-sheet flanked by nine α-helices. This
domain resembles a topology observed in a number of nucleotide anddinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)-
dependent methyltransferase (MTases) [].
This domain is found in ATP-dependent RNA helicase SUV3. It is found in bacterial and eukaryotic proteins, it is approximately 50 amino acids in length and it is usually found in association with
.
The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes [
].
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 20
comprises enzymes with only one known activity; alpha, alpha-trehalose-phosphate synthase [UDP-forming] ().
Synthesis of trehalose in the yeast Saccharomyces cerevisiae is catalysed by the trehalose-6-phosphate (Tre6P) synthase/phosphatase complex, which is composed of at least three different subunits encoded by the genes TPS1, TPS2, and TSL1. Tps1 and Tps2 carry the catalytic activities of trehalose synthesis, namely Tre6P synthase (Tps1) and Tre6P phosphatase (Tps2), while TsI1 has regulatory functions. There is some evidence that TsI1 and Tps3
may share a common function with respect to regulation and/or structural stabilisation of the Tre6P synthase/phosphatase complex in exponentially growing, heat-shocked cells [].OtsA (trehalose-6-phosphate synthase) from Escherichia coli has homology to the full-length TPS1, the N-terminal part of TPS2 and an internal region of TPS3 (TSL1) of yeast [
].
This conserved domain is found in Thyroid adenoma-associated protein (THADA) from animals and in the yeast homologue tRNA (cytidine(32)-2'-O)-methyltransferase non-catalytic subunit TRM732 [
,
,
]. Trm732 forms a complex with the methyltransferase Trm7 to 2'- O- methylate tRNA residue 32 (Nm32), being required for Trm7 methylation activity. In humans, mutations of the Trm7 homologue FTSJ1, which interacts with THADA, impair Nm32 modifications, associated with non-syndromic X-linked intellectual disability [,
,
]. It has been suggested that these proteins may play a role in additional biological processes not related to translation. This domain contains a RRSAGLP conserved motif that is required for tRNA modification activity (Funk HM et.al., Preprint from bioRxiv, 03 Jun 2021 DOI: 10.1101/2021.06.03.446962) [,
,
].
The hypoxia induced gene 1 (HIG1) or hypoglycemia/hypoxia inducible
mitochondrial protein (HIMP1) is up-regulated by stresses of themicroenvironment such as low oxygen or low glucose conditions. HIG1 is a
mitochondrial inner membrane protein, which is ubiquitously expressed. It ispredicted to be an integral membrane protein consisting of two hydrophobic
helices, 21-23 residues in length that might tend to form a hairpin-like loopacross the bilayer. HIG1 could be implied in apoptotic or cytoprotective
signals. HIG1 is a member of a well conserved eukaryote protein family. Thepredicted transmembrane helice (TMH) and loop regions represent the most
highly conserved regions in these proteins [,
].The profile we developed covers the predicted TMH and loop regions.
This domain is found in proteins thought to be involved in the response to hypoxia [
]. It is also found in altered inheritance of mitochondria proteins.
Uncharacterised protein family, basic secretory protein
Type:
Family
Description:
Proteins in this entry include basic secretory proteins (BSPs) believed to be part of the plants defence mechanism against pathogens [
]. In plants, this group of proteins are known as PR-17 family, including At2g15120 from Arabidopsis, NtPRp27 from Nicotiana tabacum and StPRp27 from potatoes [,
]. This entry also includes uncharacterised proteins from bacteria and fungi.
This entry represents the largely extracellular catalytic region of CAAX prenyl protease homologues such as Human FACE-1 protease. These are metallopeptidases, with the characteristic HExxH motif giving the two histidine-zinc-ligands and an adjacent glutamate on the next helix being the third. The whole molecule folds to form a deep groove/cleft into which the substrate can fit [
,
].This group of metallopeptidases belong to MEROPS peptidase family M48. Proteins with this domain are mostly described as probable protease htpX homologue (
) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit.
Following prenylation, proteins are subject to prenyl-dependent modifications at their C-terminal end, which are required for their subcellular targeting. The three C-terminal residues of the CAAX box prenylation signaling motif are removed before methylation of the free carboxyl group of the prenyl cysteine moiety.CAAX prenyl protease 1 (also known as Ste24p) removes the C-terminal three residues of CAAX [
,
]. It also acts to cleave the N-terminal extension of the farnesylated A-factor mating pheromone in Saccharomyces cerevisiae [,
,
].
This motif occurs C-terminal to leucine-rich repeats in "sds22-like"and "typical"LRR-containing proteins. Examples from the metazoa are described as either "Acidic leucine-rich nuclear phosphoprotein 32 family member A"or have been characterised as U2A', the protein that interacts with U2B'' facilitating the interaction with U2 snRNA. U2A' is required for the spliceosome assembly and the efficient addition of U2 snRNP onto the pre-mRNA [
]. The crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA has been described [
].
Protein phosphatases remove phosphate groups from various proteins that are
the key components of a number of signalling pathways in eukaryotes andprokaryotes. Protein phosphatases that dephosphorylate Ser and Thr residues
are classified into the phosphoprotein (PPP) and the protein phosphataseMg(2+)- or Mn(2+)-dependent (PPM) families. The core structure of PPMs is the
300-residue PPM-type phosphatase domain that catalyzes the dephosphorylationof phosphoserine- and phosphothreonine-containing protein. The PPM-type
phosphatase domain is found as a module in diverse structural contexts and ismodulated by targeting and regulatory subunits [
,
,
,
].The PP2C-type phosphatase domain consists of 10 segments of β-strands and 5
segments of α-helix and comprises a pair of detached subdomains. The firstis a small β-sandwich with strand beta1 packed against strands beta2 and
beta3; the second is a larger β-sandwich in which a four-stranded beta-heet packs against a three-stranded β-sheet with flanking α-helices [
,
].This entry represents a conserved aspartate residue involved in divalent cation binding [
].
Repressor of RNA polymerase III transcription Maf1
Type:
Family
Description:
Maf1 is a negative regulator of RNA polymerase III [
,
]. It inhibits the de novo assembly of TFIIIB onto DNA []. Maf1 represses Pol III in response to DNA damage, oxidative stress, growth to stationary phase, treatment with rapamycin or chlorpromazine, and blocking of the secretory pathway []. It targets the initiation factor TFIIIB []. Its structure has been solved [].
Aldose 1-epimerase (
) (mutarotase) is the enzyme responsible for the anomeric interconversion of D-glucose and other aldoses between their alpha- and beta-forms. Glucose-6-phosphate 1-epimerase (
) has been shown to catalyse the interconversion between the alpha and beta anomers from at least three hexose 6-phosphate sugars (Glc6P, Gal6P, and Man6P) [
].
Aldose 1-epimerase (
) (also known as mutarotase) participates in the Leloir pathway for galactose/glucose interconversion. It is the enzyme responsible for the anomeric interconversion of D-glucose and other aldoses between their alpha- and beta-forms. The sequence of mutarotase from two bacteria, Acinetobacter calcoaceticus and Streptococcus thermophilus is available [
]. The best conserved region in the sequence of mutarotase is centered around a conserved histidine residue which may be involved in the catalytic mechanism.This entry includes galactose mutarotases/aldose-1-epimerases mainly from bacteria, plants and animals []. In animals, beta-D-galactose is metabolized in the liver into glucose 1-phosphate, the primary metabolic fuel, by the action of four enzymes that constitute the Leloir pathway: GALM, GALK1 (galactokinase), GALT (galactose-1-phosphate uridylyltransferase) and GALE (UDP-galactose-4'-epimerase). A biallelic GALM variant has been identified as causing a novel type of galactosemia [].
Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA and plays a significant role during initiation, elongation, and termination of protein synthesis. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. L11 consists of a 23S rRNA binding C-terminal domain and an N-terminal domain that directly contacts protein synthesis factors. These two domains are joined by a flexible linker that allows inter-domain movement during protein synthesis. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA [,
,
,
]. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response"to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation [
,
,
,
,
,
,
,
,
,
,
,
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA and plays a significant role during initiation, elongation, and termination of protein synthesis. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. L11 consists of a 23S rRNA binding C-terminal domain and an N-terminal domain that directly contacts protein synthesis factors. These two domains are joined by a flexible linker that allows inter-domain movement during protein synthesis. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA [,
,
,
]. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.This entry represents the C-terminal domain of L11/L12. The domain consists of a three-helical bundle and a short parallel two-stranded β-ribbon, with an overall α3-β4-α4-α5-β5 topology. All five secondary structure elements contribute to a conserved hydrophobic core. The domain is characterised by two extended loops that are disordered in the absence of the RNA but have defined structures in the complex [].
Members of the Pumilio family of proteins (Puf) regulate translation and mRNA stability in a wide variety of eukaryotic organisms including mammals, flies, worms, slime mold, and yeast [
]. Pumilio family members are characterised by the presence of eight tandem copies of an imperfectly repeated 36 amino acids sequence motif, the Pumilio repeat, surrounded by a short N- and C-terminal conserved region. The eight repeats and the N- and C-terminal regions form the Pumilio homology domain (PUM-HD). The PUM-HD domain is a sequence-specific RNA binding domain. The Puf family of proteins are mainly post-transcriptional regulators. Several Puf members have been shown to bind specific RNA sequences mainly found in the 3' UTR of mRNA and repress their translation [,
]. Frequently, Puf proteins function asymmetrically to create protein gradients, thus causing asymmetric cell division and regulating cell fate specification [].Crystal structure of Pumilio repeats has been solved [
]. The PUM repeat with the N- and C-terminal regions pack together to form a right-handed superhelix that approximates a half doughnut structurally similar to the Armadillo (ARM) repeat proteins, beta-catenin andkaryopherin alpha. The RNA binds the concave surface of the molecule, whereeach of the protein's eight repeats makes contacts with a different RNA base
via three amino acid side chains at conserved positions [].This entry represents the Pumilio repeat.
The FF domain may be involved in protein-protein interaction [
]. It often occurs as multiple copies and often accompanies WW domains . PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [
].
Acetylornithine/Succinylornithine transaminase family
Type:
Family
Description:
This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from Escherichia coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (
), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine
succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism []. Members of this family may also act on ornithine, like ornithine aminotransferase () [] and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (, DapC, an enzyme of lysine biosynthesis) [
].
This family of sequences contains the 40kDa polypeptides from garlic viruses (Allexiviruses), which do not resemble any other plant virus gene products reported so far [
].Rod-shaped flexuous viruses have been isolated from garlic plants, Allium sativum. Infection by this virus creates typical mosaic symptoms. The core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues shows similarities to the corresponding 12K proteins of the potexviruses and carlaviruses []. Viral epidemics by allexiviruses are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses [].
The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate.PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [
], as well as in archaeal and eukaryotic RNA exosomes [,
], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [,
].This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes [
].
Polynucleotide phosphorylase (PNPase) is a polyribonucleotide nucleotidyl transferase
that degrades mRNA in prokaryotes. Polynucleotide phosphorylase and the Ribonuclease PH (RNase PH) family possess a common domain represented by this entry. This suggests similar structures and mechanisms of action for these 3'-->5' phosphorolytic enzymes [
]. In the case of PNPase, the core domain is found duplicated [].
The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate.PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [
], as well as in archaeal and eukaryotic RNA exosomes [,
], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [,
].This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes [
].
Proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues [
,
,
]. The best studied of these proteins is the prokaryotic catabolite gene activator (alsoknown as the cAMP receptor protein) (gene crp) where such a domain is known to be composed of three α-helices and a distinctive eight-stranded, antiparallel β-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the β-barrel. cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain,which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterised, one is found in rod cells where it plays a role in visual signal transduction.
Proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues [
,
,
]. The best studied of these proteins is the prokaryotic catabolite gene activator (alsoknown as the cAMP receptor protein) (gene crp) where such a domain is known to be composed of three α-helices and a distinctive eight-stranded, antiparallel β-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the β-barrel. cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain,
which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterised, one is found in rod cells where it plays a role in visual signal transduction.
Acyl-CoA thioesterases are a group of enzymes that catalyse the hydrolysis of acyl-CoAs to the free fatty acid and coenzyme A (CoASH). They consequently have the potential to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH. They may also be involved in the metabolic regulation of peroxisome proliferation.This family includes Acyl-CoA thioesterase 2 from Gammaproteobacteria [
], Acyl-coenzyme A thioesterase 8 from mammals [], Peroxisomal acyl-coenzyme A thioester hydrolase 1 from Saccharomyces cerevisiae [] and Acyl-CoA hydrolase 1/2 from Arabidopsis thaliana [,
].
Proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues [
,
,
]. The best studied of these proteins is the prokaryotic catabolite gene activator (alsoknown as the cAMP receptor protein) (gene crp) where such a domain is known to be composed of three α-helices and a distinctive eight-stranded, antiparallel β-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the β-barrel. cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain,which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterised, one is found in rod cells where it plays a role in visual signal transduction.
This family of eukaryotic proteinase inhibitors, belongs to MEROPS inhibitor family I12, clan IF. They predominantly inhibit serine peptidases of the S1 family (
) [
]. They play a role in defense response against pathogens and insects, but they also have been studied as therapeutic treatment in cancer and inflammatory disorders []. Exceptionally, cowpea trypsin inhibitor inhibits a cathepsin L-like cysteine proteinase CPL-1 from the nematode Heterodera glycines [].The Bowman-Birk inhibitor family [
,
] is one of the numerous families of serine proteinase inhibitors. They have a duplicated structure and generally possess two distinct inhibitory sites. These inhibitors are primarily found in plants and in particular in the seeds of legumes as well as in cereal grains. In cereals they exist in two forms, one of which is a duplication of the basic structure []. Proteins of the Bowman-Birk inhibitor family of serine proteinase inhibitors interact with the enzymes they inhibit via an exposed surface loop that adopts the canonical proteinase inhibitory conformation. The resulting non-covalent complex renders the proteinase inactive. This inhibition mechanism is common for the majority of serine proteinase inhibitor proteins and many analogous examples are known. A particular feature of the Bowman-Birk inhibitor protein, however, is that the interacting loop is a particularly well-defined disulphide-linked short β-sheet region [
,
,
].
The ~75-residue DWNN (Domain With No Name) domain is highly conserved through eukaryotic species but is absent in prokaryotes. The DWNN domain is found only at the N terminus of the RBBP6 family of proteins which includes:Mammalian RBBP6, a splicing-associated protein that plays a role in the induction of apoptosis and regulation of the cell cycle.Drosophila melanogaster (Fruit fly) SNAMA (something that sticks like glue), a protein that appears to play a role in apoptosis.All of the identified RBBP6 homologues include the DWNN domain, a CCHC-type zinc finger (see
) and a RING-type zinc finger (see
). The three domain form is found in plants, protozoa, fungi and microsporidia. The RBBP6 homologues in vertebrates, insects and worms are longer and include additional domains. In addition to forming part of the full-length RBBP6 protein, the DWNN domain is also expressed in vertebrates as a small protein containing a DWNN domain and a short C-terminal tail (RBBP6 variant 3). The DWNN domain adopts a fold similar to the ubiquitin one, characterised by two α-helices and four β-sheets ordered as β-β-α-β-α-β along the sequence. The similarity of DWNN domain to ubiquitin and the presence of the RING finger suggest that the DWNN domain may act as an ubiquitin-like modifier, possibly playing a role in the regulation of the splicing machinery [
,
].
The tryptophan RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in Bacillus sp. by binding to the leader region of the nascent trp operon mRNA [
]. The crystal structure of the Trp RNA-binding attenuation protein of Bacillus subtilis (mtrB, ) has been solved [
]. TRAP forms an oligomeric ring consisting of 11 single-domain subunits, where each subunit adopts a double-stranded β-helix structure with the appearance of a β-sandwich of distinct architecture and jelly-roll fold. The 11 subunits are stabilised by 11 inter-subunit strands, forming a β-wheel with a large central hole. TRAP is activated by binding to tryptophan in clefts between adjacent β-strands, which induces conformational changes in the protein. Activated TRAP binds an mRNA target sequence consisting of 11 (G/U)AG repeats, separated by 2-3 spacer nucleotides. The spacer nucleotides do not make direct contact with the TRAP protein, but they do influence the conformation of the RNA, which might influence the specificity of TRAP [].This superfamily represents a domain with a TRAP-like double-stranded β-helix topology. This domain is found in TRAP proteins, as well as in the hypothetical protein SPyM3_0169 from Streptococcus pyogenes. SPyM3_0169 contains 9 domains per ring-like trimer, where each subunit contains three structural repeats.
cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small β-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs [
]. In cEGFs the C-terminal thiol resides on the C-terminal β-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.
Glycoside hydrolase family 3
comprises enzymes with a number of known activities; beta-glucosidase (
); beta-xylosidase (
); N-acetyl beta-glucosaminidase (
); glucan beta-1,3-glucosidase (
); cellodextrinase(
); exo-1,3-1,4-glucanase (
).
These enzymes are two-domain globular proteins that are N-glycosylated at three sites [
]. This entry represents the C-terminal domain, involved in catalysis and may be involved in binding beta-glucan []. It is found associated with .
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 3
comprises enzymes with a number of known activities; beta-glucosidase (
); beta-xylosidase (
); N-acetyl beta-glucosaminidase (
); glucan beta-1,3-glucosidase (
); cellodextrinase (
); exo-1,3-1,4-glucanase (
).
These enzymes are two-domain globular proteins that are N-glycosylated at three sites []. This domain is often N-terminal to the glycoside hydrolase family 3, C-terminal domain .
This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self-incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties [
].
This family consists of several plant specific phytosulfokine precursor proteins. Phytosulfokines, are active as either a pentapeptide or a C-terminally truncated tetrapeptide. These compounds were first isolated because of their ability to stimulate cell division in somatic embryo cultures of Asparagus officinalis [
].
This entry represents an agenet domain found in EMSY-like (AtEML) proteins, which have possible roles in chromatin regulation and are related to the BRCA2-interacting human oncoprotein EMSY [
]. Proteins containing this domain also include MRG2 (AT1G02740) from Arabidopsis and PHD finger protein 20-like protein 1 (PHF20L1) from animals. MRG2 binds to the FLOWERING LOCUS T locus and elevates the expression in an H3K36me3-dependent manner []. The function of PHF20L1 is not clear.
Fragile X messenger ribonucleoprotein 1 (FMR1/FMRP), and its autosomal paralogues, RNA-binding proteins FXR1/2 (Fragile X-related protein 1/2), comprise a family of RNA-binding proteins that are involved the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs, playing a crucial role in neuronal development and synaptic plasticity [
,
,
,
]. These proteins are highly similar to one another and also retain highly conserved domain architecture. The two ribonucleoprotein K homology (KH) domains and the cluster of arginine and glycine residues that constitute the RGG box, comprise a large region that is important for RNA binding and polyribosome association. In addition, two Agenet-like domains exist in tandem within the N-terminal regions of FMRP family proteins. The Agenet-like domain belongs to the "Royal"domain superfamily which contains also the Tudor, chromo, MBT, PWWP and plant Agenet domains. Biochemical analysis of the tandem Agenet-like domains reveals their ability to preferentially recognise trimethylated peptides in a sequence-specific manner [
,
,
,
].The Agenet-like domain folds into a bent four-stranded antiparallel β-sheet with a fifth strand closing the cavity of the sheet, similar to a thumb across a semiclosed hand [
,
].
This leucine-zipper domain can be found in MIP1 proteins and in putative Rho GTPase-activating proteins. MIP1 proteins, here largely from plants, are subunits of the TORC2 (rictor-mTOR) protein complex controlling cell growth and proliferation [
]. The leucine-zipper is likely to be the region that interacts with plant MADS-box factors [],
An Escherichia coli gene designated purU has been identified and characterised. The gene codes for a 280-amino-acid protein, PurU (
,
). PurU is an enzyme that catalyses the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate
[,
].10-formyltetrahydrofolate + H(2)O = formate +tetrahydrofolate Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer of 32kDa subunits, is activated by methionine and inhibited by glycine. Heterotropic cooperativity is observed for activation by methionine in the presence of glycine and for inhibition by glycine in the presence of methionine. These results suggest that formyl-FH4 hydrolase is a regulatory enzyme whose main function is to balance the pools of FH4 and C1-FH4 in response to changing growth conditions. The enzyme uses methionine and glycine to sense the pools of C1-FH4 and FH4, respectively.This entry also includes PurU from Arabidopsis, which is involved in photorespiration. It prevents the excessive accumulation of 5-formyl tetrahydrofolate (THF), a potent inhibitor of the Gly decarboxylase/Ser hydroxymethyltransferase complex [
].
This domain describes a pleckstrin homology (PH)-like region found in several plant proteins, including VAN3-binding protein from Arabidopsis thaliana (also known as FORKED1), a component of the auto-regulatory loop which enables auxin canalisation by recruitment of the PIN1 auxin efflux protein to the cell membrane [
].
This domain can be found at the N-terminal end of several plant proteins, including VAN3-binding protein from Arabidopsis thaliana (also known as FORKED1), a component of the auto-regulatory loop which enables auxin canalisation by recruitment of the PIN1 auxin efflux protein to the cell membrane [
]. This domain is frequently found on proteins containing at the C terminus.
In general, the Gfo/Idh/MocA protein family members are enzymes that catalyse various different chemical reactions such as oxidation and reduction of carbohydrates, oxidation of trans-dihydrodiols, reduction of biliverdin, and hydrolysation of glycosidic bonds. All the enzymes in this family utilise NAD(P) as a hydride donor or acceptor. However, despite the structural similarities, some member such as the transcriptional repressor Gal80p, does not have enzymatic activity [
]. The Gfo/Idh/MocA protein family members consists of two main domains: an N-terminal dinucleotide-binding domain containing a typical Rossmann fold3 and a C-terminal alpha/beta-domain participating in substrate binding and oligomerisation. This entry represents the C-terminal domain [
].
This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family (GFO: glucose--fructose oxidoreductase, IDH: inositol 2-dehydrogenase and MOCA which catalyses a dehydrogenase reaction involved in rhizopine catabolism) in UniProtKB/Swiss-Prot, which includes enzymes that catalyse different chemical reactions such as oxidation and reduction of carbohydrates, oxidation of trans-dihydrodiols, reduction of biliverdin and hydrolysation of glycosidic bonds [
]. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes, although it does not have enzymatic activity; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis.The Gfo/Idh/MocA protein family members have very low sequence identity but the 3D structures of the proteins are very similar, consisting of two main domains: an N-terminal dinucleotide-binding domain containing a typical Rossmann fold3 and a C-terminal α/β-domain participating in substrate binding and oligomerisation. This entry represents the N-terminal domain [].
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 [
,
].A number of eukaryotic and archaebacterial ribosomal proteins can be grouped
on the basis of sequence similarities []. One of these families consists of:Mammalian L15.Insect L15.Plant L15.Yeast YL10 (L13) (Rp15r).Archaebacterial L15e.These proteins have about 200 amino acid residues.
A number of eukaryotic and archaebacterial ribosomal proteins can be grouped
on the basis of sequence similarities []. One of these families consists of:Mammalian L15.Insect L15.Plant L15.Yeast YL10 (L13) (Rp15r).Archaebacterial L15e.These ribosomal proteins have a structure corresponding to a 3-layer (α-β-alpha) sandwich.
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 [
,
].A number of eukaryotic and archaebacterial ribosomal proteins can be grouped
on the basis of sequence similarities []. One of these families consists of:Mammalian L15.Insect L15.Plant L15.Yeast YL10 (L13) (Rp15r).Archaebacterial L15e.These proteins have about 200 amino acid residues.This entry represents a short conserved sequence region located in the central section of these proteins.
Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain
Type:
Domain
Description:
Biotin and lipoic acid are the covalently bound cofactors of various
multicomponent enzyme complexes that catalyse key metabolic reactions. Inthese enzymes complexes, biotin and lipoic acid are attached via amide linkage
through their carboxyl group and the ε-amino group of a specific lysineresidue of a protein module known respectively as the biotinyl and the lipoyl
domain. Covalent attachment of biotin and lipoic acid tothese enzyme complexes occurs post-translationally, and it is mediated by
biotinylating and lipoylating protein enzymes, which specifically recognisethe biotinyl and lipoyl domains, ensuring their correct post-translational
modification. Lipoylating and biotinylating enzymes are evolutionarily relatedprotein families containing a homologous catalytic module [
].Amino acid sequence conservation between the catalytic modules of biotinyl
protein ligases (BPLs) and lipoyl protein ligases (LPLs) is very low, andmainly affects residues that are important for the scaffold of the structure,
such as those contributing to the hydrophobic core. Despite the poor overallsequence similarity, a single lysine residue is strictly conserved in all LPL
and BPL sequences. This lysine residue is likely to bind specifically to thecarbonyl oxygen of the carboxyl group of biotin or at the end of the hydrogen-
carbon tail of the lipoyl moiety []. The BPL/LPL catalytic domain contains aseven-stranded mixed β-sheet on one side and four α-helices on the
other side [].
Lipoate-protein ligase B [
] (gene lipB), alternatively known as octanoyltransferase () is an enzyme that creates an amide linkage that joins the free carboxyl group of lipoic acid to the ε-amino group of a specific lysine residue in lipoate-dependent enzymes.
octanoyl-[acyl-carrier-protein] + protein = protein N6-(octanoyl)lysine + acyl carrier proteinLipoyl(octanoyl) transferase catalyses the first committed step in the biosynthesis of lipoyl cofactor. The lipoyl cofactor is essential for the function of several key enzymes involved in oxidative metabolism, as it converts apoprotein into the biologically active holoprotein. Examples of such lipoylated proteins include pyruvate dehydrogenase (E2 domain), 2-oxoglutarate dehydrogenase (E2 domain), the branched-chain 2-oxoacid dehydrogenases and the glycine cleavage system (H protein) [
]. Lipoyl-ACP can also act as a substrate [] although octanoyl-ACP is likely to be the true substrate []. The other enzyme involved in the biosynthesis of lipoyl cofactor is , lipoyl synthase. An alternative lipoylation pathway involves
, lipoate-protein ligase, which can lipoylate apoproteins using exogenous lipoic acid (or its analogues).
Such an enzyme has also been found in fungi [
], where it is located in the mitochondria. It also seems to exist in plants [] and is encoded in the chloroplast genome of the red alga Cyanidium caldarium [].
Lipoate-protein ligase B [
] (gene lipB), alternatively known as octanoyltransferase () is an enzyme that creates an amide linkage that joins the free carboxyl group of lipoic acid to the ε-amino group of a specific lysine residue in lipoate-dependent enzymes.
octanoyl-[acyl-carrier-protein] + protein = protein N6-(octanoyl)lysine + acyl carrier proteinLipoyl(octanoyl) transferase catalyses the first committed step in the biosynthesis of lipoyl cofactor. The lipoyl cofactor is essential for the function of several key enzymes involved in oxidative metabolism, as it converts apoprotein into the biologically active holoprotein. Examples of such lipoylated proteins include pyruvate dehydrogenase (E2 domain), 2-oxoglutarate dehydrogenase (E2 domain), the branched-chain 2-oxoacid dehydrogenases and the glycine cleavage system (H protein) [
,
]. Lipoyl-ACP can also act as a substrate [] although octanoyl-ACP is likely to be the true substrate []. The other enzyme involved in the biosynthesis of lipoyl cofactor is , lipoyl synthase. An alternative lipoylation pathway involves
, lipoate-protein ligase, which can lipoylate apoproteins using exogenous lipoic acid (or its analogues).
Such an enzyme has also been found in fungi [
], where it is located in the mitochondria. It also seems to exist in plants [] and is encoded in the chloroplast genome of the red alga Cyanidium caldarium [].This entry represents a conserved region, located in the central part of the enzyme; this region contains one of two conserved histidines.
Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalysed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studies, which show a close structural homology to other known methyltransferases [
].This group of proteins includes Ribosomal RNA small subunit methyltransferase E (RsmE) from Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [
,
]. This enzyme has two distinct but structurally related domains: the N-terminal PUA domain and the conserved MTase domain at the C-terminal end. This protein adopts a dimeric configuration that is functionally critical for substrate binding and catalysis [].
Photosystem I reaction centre subunit N, chloroplastic
Type:
Family
Description:
Photosystem I reaction centre subunit N (PSAN, also known as PSI-N) may function in mediating the binding of the antenna complexes to the PSI reaction centre and core antenna [
]. PSI-N subunit does not bind pigments [].
The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate [
]. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation [].DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) [
].This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended β-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [
].
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a domain presumed to be a zinc binding domain. The following pattern describes the zinc finger:C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C
where X can be any amino acid, and numbers in brackets indicate the number of residues. The two position can be either His or Cys. This central cysteine-rich portion encodes the DNA-binding domain which is highly conserved in eukaryotes [
]. The NFX1 family of proteins may have additional roles mediated by protein-protein interactions regarding the reiterated RING finger motifs in this central domain which strongly suggest that NFX1 is a probable E3 ubiquitin protein ligase []. This domain is found in the human transcriptional repressor NK-X1, a repressor of HLA-DRA transcription []; the Drosophila shuttle craft protein, which plays an essential role during the late stages of embryonic neurogenesis and has been shown to be a DNA- or RNA-binding protein [
]; and the yeast FKBP12-associated protein 1 (FAP1) [].
Glutamine synthetase (
) (GS) [
] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine.There seem to be three different classes of GS [
,
,
]:Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see ).
Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast.Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes.While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.This entry represents the glycine-rich region, which is thought to be involved in ATP-binding.
Glutamine synthetase (
) (GS) [
] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine.There seem to be three different classes of GS [
,
,
]:Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see
).
Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast.Class III enzymes (GSIII) has, currently, only been found in Bacteroides fragilis and in Butyrivibrio fibrisolvens. It is a hexamer of identical chains. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes.While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.This entry represents a conserved tetrapeptide in the N-terminal section of the enzyme.
Glutamine synthetase (
) (GS) [
] plays an essential role in the metabolism of nitrogen by catalysing the condensation of glutamate and ammonia to form glutamine.There seem to be three different classes of GS [
,
,
]:Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see
).
Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast.Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes.While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.This entry represents the C-terminal catalytic domain of GS enzymes.
Glutamine synthetase (
) (GS) [
] plays an essential role in the metabolism of nitrogen by catalysing the condensation of glutamate and ammonia to form glutamine. This entry represents the glutamine synthetase N-terminal domain, which adopts a β-grasp fold [] and contributes to the substrate binding pocket of the enzyme [,
].
Aspartyl tRNA synthetase
is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module [
]. Asparagine tRNA ligase (
) is also an alpha2 dimer that belongs to class IIb. There are remarkable similarities between the tertiary structures of asparaginyl-tRNA synthetase and aspartyl-tRNA synthetase [
].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 [].
DNA replication in eukaryotes results from a highly coordinated interaction between proteins, often as part of protein complexes, and the DNA template. One of the key early steps leading to DNA replication is formation of the prereplication complex, or pre-RC. The pre-RC is formed by the sequential binding of the origin recognition complex (ORC), Cdc6 and Cdt1 proteins, and the MCM complex. Activation of the pre-RC into the initiation complex (IC) is achieved via the action of S-phase kinases, eventually leading to the loading of the replication machinery.Recently, a novel replication complex, GINS (for Go, Ichi, Nii, and San; five, one, two, and three in Japanese), has been identified [
,
]. The precise function of GINS is not known. However, genetic and two-hybrid interactions indicate that it mediates the loading of the enzymatic replication machinery at a step after the action of the S-phase kinases []. Furthermore, GINS may be a part of the replication machinery itself, since it is found associated with replicating DNA [,
]. Electron microscopy of GINS shows that it forms a ring-like structure [], reminiscent of the structure of PCNA [], the DNA polymerase delta replication clamp.This observation, coupled with the observed interactions for GINS, indicates that the complex may represent the replication clamp for DNA polymerase epsilon [].This family of proteins represents the PSF1 component (for partner of SLD five) of the GINS complex.
Dihydroorotate dehydrogenase (
) (DHOdehase) catalyses the fourth step in the
de novobiosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria [
].This entry represents a domain found in the type I dihydroorotate dehydrogenases and dihydropyrimidine dehydrogenase.
Dihydroorotate dehydrogenase (DHOD), also known as dihydroorotate oxidase, catalyses the fourth step in de novo pyrimidine biosynthesis, the stereospecific oxidation of (S)-dihydroorotate to orotate, which is the only redox reaction in this pathway. DHODs can be divided into two mains classes: class 1 cytosolic enzymes found primarily in Gram-positive bacteria, and class 2 membrane-associated enzymes found primarily in eukaryotic mitochondria and Gram-negative bacteria [
].The class 1 DHODs can be further divided into subclasses 1A and 1B, which differ in their structural organisation and use of electron acceptors. The 1A enzyme is a homodimer of two PyrD subunits where each subunit forms a TIM barrel fold with a bound FMN cofactor located near the top of the barrel [
]. Fumarate is the natural electron acceptor for this enzyme. The 1B enzyme, in contrast is a heterotetramer composed of a central, FMN-containing, PyrD homodimer resembling the 1A homodimer, and two additional PyrK subunits which contain FAD and a 2Fe-2S cluster []. These additional groups allow the enzyme to use NAD(+) as its natural electron acceptor.
The class 2 membrane-associated enzymes are monomers which have the FMN-containing TIM barrel domain found in the class 1 PyrD subunit, and an additional N-terminal alpha helical domain [
,
]. These enzymes use respiratory quinones as the physiological electron acceptor.
This entry represents protein arginine N-methyltransferase PRMT7 [
].PRMT7 can catalyze the formation of omega-N monomethylarginine (MMA) and symmetrical dimethylarginine (sDMA), with a preference for the formation of MMA. It mediates the symmetrical dimethylation of arginine residues in the small nuclear ribonucleoproteins Sm D1 (SNRPD1) and Sm D3 (SNRPD3); such methylation being required for the assembly and biogenesis of snRNP core particles. It also mediates the symmetric dimethylation of histone H4 'Arg-3' to form H4R3me2s. It plays a role in gene imprinting by being recruited by CTCFL at the H19 imprinted control region (ICR) and methylating histone H4 to form H4R3me2s, possibly leading to recruit DNA methyltransferases at these sites. It may also play a role in embryonic stem cell (ESC) pluripotency [
,
,
,
].
Protein arginine methyltransferases (PRMTs) are enzymes that transfer methyl groups to the arginine residues of histones and other proteins. Arginine methylation is an important posttranslational modification process that plays functional roles in transcriptional control, splicing, DNA repair, and signaling [
,
,
]. PRMTs use S-adenosylmethionine(SAM or AdoMet)-dependent methylation to modify the guanidino nitrogens of the arginine side chain by adding one or two methyl groups [
]. According to their methylation status, the PRMT enzymes are classified into different group types. While the type-I PRMT enzymes catalyse the formation of monomethylarginine (MMA) and asymmetric dimethylarginine (aDMA), the type-II PRMT enzymes form MMA and symmetric dimethylarginine (sDMA). The enzymes PRMT1, PRMT3, PRMT4, PRMT6 and PRMT8 belong to the type-I and PRMT5, PRMT7 and PRMT9 to type-II.
This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. It is a component of a complex containing Cef1 and may be involved in pre-mRNA splicing [
].
Guanine nucleotide binding protein (G-protein), alpha subunit
Type:
Family
Description:
Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (
), beta (
) and gamma (
) [
]. G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins or by covalent modifications [].G protein alpha subunits are 350-400 amino acids in length and have
molecular weights in the range 40-45kDa. Seventeen distinct types ofalpha subunit have been identified in mammals. These fall into 4 main
groups on the basis of both sequence similarity and function: alpha-S (),
alpha-Q (), alpha-I (
)and alpha-12(
) [
].The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [,
]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions.This family consists of the G protein alpha subunit, which acts as a weak GTPase. G protein classes are defined based on the sequence and function of their alpha subunits, which in mammals fall into four main categories: G alpha-S (
), G alpha-Q (
), G alpha-I (
) and G alpha-12 (
); there are also fungal (
) and plant classes (
) of alpha subunits.
Many alpha subunits are substrates for ADP-ribosylation by cholera or pertussis toxins. They are often N-terminally acylated, usually with myristate and/or palmitoylate, and these fatty acid modifications are probably important for membrane association and high-affinity interactions with other proteins. The alpha subunit consists of two domains: a GTP-binding domain and a helical insertion domain (
). The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The switch regions are loops of α-helices with conformations sensitive to guanine nucleotides. The helical insertion domain is inserted into the GTP-binding domain before switch region I and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation.
Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (
), beta (
) and gamma (
) [
]. G proteins act as signal transducers, relaying a signal from a ligand-activated GPCR (G protein-coupled receptor) to an enzyme or ion channel effector. The activated GPCR promotes the exchange of GDP for GTP on the G protein alpha subunit, allowing the trimeric G protein to be released from the receptor and to dissociate into active (GTP-bound) alpha subunit and beta/gamma dimer, both of which activate distinct downstream effectors. There are several isoforms of each subunit, which together can makeup hundreds of combinations of G proteins, each one linking a specific receptor to a certain effector.The heterotrimeric G protein alpha subunit is composed of two domains: a GTP-binding domain and a helical insertion domain. The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The helical insertion domain is inserted into the GTP-binding domain before switch region I, and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation []. This superfamily represents the G protein alpha subunit helical insertion domain.
Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in
animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts.PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. Pex19 is involved in membrane assembly and maintenance and functions as a receptor and chaperone of peroxisomal membrane proteins (PMPs) [
].
Histone acetylation is required in many cellular processes including transcription, DNA repair, and chromatin assembly. This family contains the fungal RTT109 protein, which is required for H3K56 acetylation [
]. In Schizosaccharomyces pombe (Fission yeast) loss of RTT109 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin []. RTT109 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of Pol II in yeast []. This family also includes p300/CBP acetyltransferase, which has different catalytic properties and cofactor regulation to RTT109 []. CREB-binding protein (CBP) is a transcriptional co-activator that acetylates both histones and non-histone proteins [,
,
]. CBP binds specifically to phosphorylated CREB and enhances its transcriptional activity toward cAMP-responsive genes [,
].
This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. The majority of the members in this entry carry the exopeptidase active-site residues of Ser-122, Asp-239 and His-269 as in
.
The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB [
]. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs [].
L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of
L-lactate to pyruvate, the last step in anaerobic glycolysis []. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate []. The enzyme participates in the citric acid cycle.This entry represents the N-terminal, and is thought to be a Rossmann NAD-binding fold.
This entry represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme functions as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified [
] which can discriminate between the two activities.
NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes functions as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified [
] which can discriminate between the two activities.This entry represents the active site of L-lactate dehydrogenase, and includes a conserved histidine which is essential to the catalytic mechanism.
A number of autophagy-related proteins have been identified in yeast, including the key autophagic protein Atg8, which is a ubiquitin-like protein with a structure consisting of two amino-terminal α-helices and a ubiquitin-like core [
,
]. Many other eukaryotes contain multiple Atg8 orthologues. Atg8 genes of multicellular animals can be divided into three subfamilies: microtubule-associated protein 1 light chain 3 (MAP1LC3 or LC3) [], gamma-aminobutyric acid receptor-associated protein (GABARAP) and Golgi-associated ATPase enhancer of 16kDa (GATE-16) [,
]. Family members are involved in diverse intracellular trafficking and autophagy processes.
This entry represents a 45 residue conserved domain found at the N-terminal end CIR protein (CBF1-interacting co-repressor, also known as corepressor interacting with RBPJ 1). This domain can be found in the fungal CWC25 family members and mammlian LENG1 (leukocyte receptor cluster member 1) protein.CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex [
]. CIR also plays a role in alternative splicing []. Budding yeast Cwc25 is a pre-mRNA-splicing factor involved in pre-mRNA splicing [
].
This entry represents a conserved plant aminotransferase-like domain which is similar to a DNA binding motif found in transposases [
,
]. This domain is found in Protein MAINTENANCE OF MERISTEMS (MAIN) and its three homologues MAIN-like 1/2/3 from Arabidopsis [], which are thought to be encoded by transposon-derived genes, involved in maintaining genomic stability and function, possibly by controlling heterochromatic elements [].
Adenine phosphoribosyltransferase (APRTase,
) is a widely distributed enzyme, and its deficiency in humans causes the accumulation of
2,8-dihydroxyadenine. It is the sole catalyst for adenine recycling in most eukaryotes.AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate
Pleckstrin homology (PH) domains are small modular domains that occur in a large variety of proteins and they have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner, enabling them to interact with other components of signal transduction pathways. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. The domains can bind phosphatidylinositol within biological membranes and proteins such as the beta/gamma subunits of heterotrimeric G proteins [] and protein kinase C []. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to phosphoinositide phosphates (PIPs) with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminal of the domain, which are not conserved across all PH domains [,
,
].PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.The 3D structure of several PH domains has been determined [
]. All known cases have a common structure consisting of two perpendicular anti-parallel β-sheets, followed by a C-terminal amphipathic helix. The loops connecting the β-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain.Proteins reported to contain one more PH domains belong to the following families:Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains.Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family.Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily.Insulin Receptor Substrate 1 (IRS-1).Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr.Cytoskeletal proteins such as dynamin (see
), Caenorhabditis elegans kinesin-like protein unc-104 (see
), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1.
Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see
) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues.
Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w.Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac.Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1).C. elegans protein MIG-10.C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12.S. cerevisiae hypothetical proteins YBR129c and YHR155w.
This domain is found associated with PX domains. The PX (phox) domain [
] occurs in a variety of eukaryotic proteins associated with intracellular signalling pathways.
The PX (phox) domain [
] occurs in a variety of eukaryotic proteins and have been implicated in highly diverse functions such as cell signalling, vesicular trafficking, protein sorting and lipid modification [,
,
,
]. PX domains are important phosphoinositide-binding modules that have varying lipid-binding specificities []. The PX domain is approximately 120 residues long [], and folds into a three-stranded β-sheet followed by three -helices and a proline-rich region that immediately preceeds a membrane-interaction loop and spans approximately eight hydrophobic and polar residues. The PX domain of neutrophil cytosol factor 1 (p47phox) binds to the SH3 domain in the same protein []. Phosphorylation of p47(phox), a cytoplasmic activator of the microbicidal phagocyte oxidase (phox), elicits interaction of p47(phox) with phoinositides. The protein phosphorylation-driven conformational change of p47(phox) enables its PX domain to bind to phosphoinositides, the interaction of which plays a crucial role in recruitment of p47(phox) from the cytoplasm to membranes and subsequent activation of the phagocyte oxidase. The lipid-binding activity of this protein is normally suppressed by intramolecular interaction of the PX domain with the C-terminal Src homology 3 (SH3) domain [].The PX domain is conserved from yeast to human. A multiple alignment of representative PX domain sequences from eukaryotic proteins [
], shows relatively little sequence conservation, although their structure appears to be highly conserved. Although phosphatidylinositol-3-phosphate (PtdIns(3)P) is the primary target of PX domains, binding to phosphatidic acid, phosphatidylinositol-3,4-bisphosphate (PtdIns(3,4)P2), phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2), phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2), and phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3) has been reported as well. The PX-domain is also a protein-protein interaction domain [].
The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. It is normally about 70 amino acids in length. It is thought to be an intracellular protein-binding or lipid-binding signalling domain, which has an important function in membrane-associated processes. The structure of the GRAM domain is similar to that found in PH domains [
]. Mutations in the GRAM domain of myotubularins cause a muscle disease, which suggests that the domain is essential for the full function of the enzyme []. Myotubularin-related proteins are a large subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids [].
SelM and Sep15 consists of one catalytic a-domain that assumes a thioredoxin-like fold composed of a mixed four-stranded β-sheet and three interspersed α-helices. The active-site redox motifs of SelM and Sep15 are located between the C terminus of strand beta1 and the N terminus of helix alpha1. SelM and Sep15 may function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum [
].
The helix-hairpin-helix (HhH) motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins. The HhH motif is similar to, but distinct from, the helix-turn-helix (HtH) and the helix-loop-helix (HLH) motifs. All three motifs have two helices (H1 and H2) connected by a short turn. DNA-binding proteins with a HhH structural motif are involved in non-sequence-specific DNA binding that occurs via the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups. These HhH motifs are observed in DNA repair enzymes and in DNA polymerases. By contrast, proteins with a HtH motif bind DNA in a sequence-specific manner through the binding of H2 with the major groove; these proteins are primarily gene regulatory proteins. DNA-binding proteins with the HLH structural motif are transcriptional regulatory proteins and are principally related to a wide array of developmental processes [
].Examples of proteins that contain a HhH motif include the eukaryotic/prokaryotic RAD2 family of 5'-3' exonucleases such as T4 RNase H and T5 [
,
], eukaryotic 5' endonucleases such as FEN-1 (Flap) [], and some viral exonucleases.
The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (
) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [
,
,
]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families.In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (
) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures.
This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an α-helical arch [
,
].
This entry represents the H3TH (helix-3-turn-helix) domain of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologues. Taq (Thermus aquaticus) DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands [
,
]. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp [].
This entry represents flap endonucleases from eukaryotes, bacteria, viruses and archaea. Flap endonucleases (FENs) catalyse the exonucleolytic hydrolysis of blunt-ended duplex DNA substrates and the endonucleolytic cleavage of 5'-bifurcated nucleic acids at the junction formed between single and double-stranded DNA [
].In prokaryotes, the essential FEN reaction can be performed by the N-terminal 5'-3' exonuclease domain present on DNA polymerase I. Some eubacteria, however, possess a second gene encoding a 5'-3' exonuclease domain [
,
]. Two distinct classes of these independent bacterial FENs exist: Xni (ExoIXI) from Escherichia coli and SaFEN (Staphylococcus aureus FEN). SaFEN has both FEN and 5'-3' exonuclease activities. Xni (ExoIX) was previously identified as a 3'-5' exonuclease and named exonuclease IX (exonuclease 9) [,
] but subsequently found to possess flap endonuclease activity, but not exonuclease activity [,
,
].Archaea, eukaryotes, bacteriophages and some viruses encode a separate FEN enzyme but lack FEN domains on their DNA polymerases [
]. Escherichia phage T5 encodes the flap endonuclease D15, which catalyzes both the 5'-exonucleolytic and structure-specific endonucleolytic hydrolysis of DNA branched nucleic acid molecules [,
,
]. In bacteriophage T4, disruption of the rnh gene (which encodes a FEN, known historically as T4 RNase H) results in slower, less accurate DNA replication. Bacteriophage T4 has both 5' nuclease and flap endonuclease activities [].
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 [
,
].Rsm22 has been identified as a mitochondrial small ribosomal subunit [
] and is a methyltransferase. In Schizosaccharomyces pombe (Fission yeast), Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria []. This entry consists of mitochondrial Rsm22 and homologous sequences from bacteria.
Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein. In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre. Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units [
]. The C-terminal region of the protein is known to form a dimer. Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae (). Met 224 is also thought to play a role in copper transfer or stabilising the copper site [
].
Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La. The La protein is a 47kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome [
]. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor []. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation []. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis []. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif [].Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [
].This domain is found at the N terminus of La RNA-binding proteins as well as other proteins [
].
The La protein is a 47kDa polypeptide that often acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome patients [
]. It occurs in both the nucleus and the cytoplasm, where it takes on different roles []. In the nucleus, La facilitates the production of tRNAs, acting as a RNA polymerase III (RNAP III) transcription factor by binding to the U-rich 3'UTR of nascent transcripts, assisting in their folding and maturation []. In the cytoplasm, La facilitates the translation of specific mRNAs, acting as a translation factor. As a RNA binding protein (RBP), La associates with subsets of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis. The binding of La to specific classes of RNA molecules regulates their downstream processing, protects them from endonuclease digestion, and organises their export from the nucleus [,
,
,
].
