This entry represents a domain found in the N terminus of the pre-rRNA-processing protein Ipi1. This domain can also be found in testis-expressed sequence 10 protein (TEX10).In Saccharomyces cerevisiae, Ipi1 is a component of the RIX1 complex required for processing of ITS2 sequences from 35S pre-rRNA [
,
]. In humans, TEX10 is a component of some MLL1/MLL complex, a protein complex that can methylate lysine-4 of histone H3 [
].
In plants, this family is involved in mitochondrial fission. It binds to dynamin-related proteins and plays a role in their relocation from the cytosol to mitochondrial fission sites [
]. Its function in bacteria is unknown.
This family represents Ffh (Fifty-Four Homologue), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA [
,
]. Ffh is a GTPase homologous to eukaryotic SRP54.
Fis1 is an outer mitochondrial membrane protein that plays a role in mitochondrial membrane fission [
]. In Saccharomyces cerevisiae, it facilitates mitochondrial fission by forming protein complexes with Dnm1 and Mdv1 []. It contains tetratrico-peptide repeat (TPR)-like domain and a C-terminal transmembrane region [,
].
Proteins in this entry include HesB, IscA, SufA and ErpA, and appear to be scaffold proteins upon which 2Fe-2S clusters are assembled and subsequently transferred to acceptor proteins. Several multiprotein complexes, referred to as ISC, SUF, and NIF, are known to be necessary for building and inserting Fe-S clusters into cellular targets [
]. The HesB proteins are associated with the nif gene cluster. The Escherichia coli SufA protein is associated with SufS, a NifS homologue, and SufD which are involved in the FeS cluster assembly of the FhnF protein []. The Azotobacter protein IscA (homologues of which are also found in E. coli) is associated which IscS, another NifS homologue, and IscU, a NifU homologue, as well as other factors consistent with a role in FeS cluster chemistry []. ErpA is required, together with IscA, for the delivery of iron-sulphur clusters to the hydrogen-oxidizing [NiFe]-hydrogenases in Escherichia coli [
,
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].This presumed domain is found at the N terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [
].
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 [
,
].Eukaryotic ribosomal protein, L7, contains an N-terminal bZIP DNA binding domain and a second, DNA-binding domain has been mapped to the 50 C-terminal amino acids of the protein [
]. In addition to its role in translation, L7 has also been shown to be involved in nuclear-receptor mediated transcriptional control. There is no bacterial homologue of this protein.
This entry includes SKP1 from yeasts, animals and plants. Mammlian S-phase kinase-associated protein 1 (SKP1) is an essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription [
]. It is also part of the ubiquitin E3 ligase complex (Skp1-Pam-Fbxo45) that controls the core epithelial-to-mesenchymal transition-inducing transcription factors [].Budding yeast Skp1 is a kinetochore protein found in several complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA [
], and the RAVE complex that regulates assembly of the V-ATPase []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 [].Arabidopsis Skp1 is part of the Skp1/Cullin1/F-box protein COI1 (SCFCOI1) E3 ubiquitin ligase complex required for vegetative and floral organ development as well as for male gametogenesis [
,
]. 21 Skp1-related genes, called Arabidopsis-SKP1-like (ASK), have been uncovered in the Arabidopsis genome. They may collectively perform a range of functions and may regulate different developmental and physiological processes [,
].
Ribonuclease E and ribonuclease G are related enzymes that cleave a wide variety of RNAs [
]. RNA-binding protein AU-1 binds to RNA loop regions that are with AU-rich sequences [
].This entry represents ribonuclease E/G and RNA-binding protein AU-1.
Nucleolar GTP-binding protein 1 is involved in the biogenesis of the 60S ribosomal subunit [
]. It is found as part of the pre-60S complex in nucleolus [].
This family consists of the urease accessory protein, UreF. The urease enzyme (urea amidohydrolase) hydrolyses urea into ammonia and carbamic acid [
]. UreF is proposed to modulate the activation process of urease by eliminating the binding of nickel irons to noncarbamylated protein [].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].The genomic structure and sequence of the human ribosomal protein L7a has been determined and shown to
resemble other mammalian ribosomal protein genes []. The sequence of a gene for ribosomal protein L4 of yeast has also been determined; its single open reading frame is highly similar
to mammalian ribosomal protein L7a [,
]. Several other ribosomal proteins have been found to share sequence similarity with L7a, including Saccharomyces cerevisiae NHP2 [
], Bacillus subtilis hypothetical protein ylxQ, Haloarcula marismortui Hs6, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1203.
This entry includes the fungal vacuolar fusion protein Ccz1 which forms a complex with Mon1. The CCZ1-MON1 complex acts where vesicles fuse with the vacuole and is required in several vacuolar delivery pathways including autophagy, pexophagy and endocytosis as well cytoplasm to vacuole transport [
,
,
]. Ccz1 interacts with a GTPase during fusion [].
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 S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44).This entry represents the N-terminal domain of ribosomal protein S5, which has an α-β(3)-α structure that folds into two layers, α/β.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.
This entry represents the C-terminal of the ribosomal protein S5, which is related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (
). Ribosomal protein S5 is one of the proteins from the small ribosomal subunit.
In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies.
The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA [
]. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [
] has revealed that S17 has virtually no groups exposed on the ribosomal surface.This entry represents archaeal ribosomal S17 proteins and some homologous eukaryotic ribosomal S11 sequences.
MOZART1 or Mzt1 is a component of the gamma-tubulin complex and is required for its recruitment to the microtubule organizing centre in humans and yeast [
,
,
]. This function is conserved in plant homologues, known as gamma-tubulin complex protein 3 (GCP3)-interacting proteins (GIPs) [,
]. Studies in plant homologues GIP1 and GIP2 indicate that they play a major role in nuclear envelope shaping in both cycling and differentiated cells [] and that they are essential for centromere architecture [,
].
The proteins in this entry are highly conserved in species ranging from archaea to vertebrates and plants [
]. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS, OMIM 260400) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition []. SBDS is required for the assembly of mature ribosomes and ribosome biogenesis [].Homologue of SBDS from budding yeast is known as Sdo1, which is a guanine nucleotide exchange factor (GEF) involved in ribosome maturation. Together with the EF-2-like GTPase RIA1 (EfI1), it triggers the GTP-dependent release of TIF6 from 60S pre-ribosomes in the cytoplasm, allowing the assembly of mature ribosomes [
].
In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins [
].ClpS is a small alpha/beta protein that consists of three α-helices connected to three antiparallel β-strands [
]. The protein has a globular shape, with a curved layer of three antiparallel α-helices over a twisted antiparallel β-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue β-strand, which is flanked by two other β-strands in a small β-sheet.
Tubulin tyrosine ligase like 12 (TTLL2) is a member of the tubulin tyrosine ligase (TTL) family. Its function is not clear. It has both SET-like and TTL-like domains, suggesting histone methylation and tubulin tyrosine ligase activities. However, this protein does not have catalytic functions related to tubulin and histone modification, though it seems to have a regulatory role in these processes [
].
The enhancer of polycomb gene of Drosophila encodes a chromatin protein conserved in yeast and mammals [
]. The homologous yeast protein, known as enhancer of polycomb-like protein 1 (Epl1), is a subunit of the NuA4 histone acetyltransferase (HAT) complex, which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A []. Epl1 also found in a novel highly active smaller complex named Piccolo NuA4 (picNuA4), which strongly prefers chromatin over free histones as substrate []. The NuA4 HAT complex is highly conserved in eukaryotes, and it plays primary roles in transcription, cellular response to DNA damage, and cell cycle control [].This entry represents all eukaryotic enhancer of polycomb proteins, including enhancer of polycomb-like proteins.
This entry includes protein from blue-green algae and plants, including CRR7 (Chlororespiratory reduction 7) protein from Arabidopsis. CRR7 is part of the chloroplastic NAD(P)H dehydrogenase complex (NDH Complex) involved in respiration, photosystem I (PSI) cyclic electron transport and CO2 uptake [
]. It is essential for the stable formation of the NDH Complex [].
This conserved hypothetical protein family with four predicted transmembrane regions is found in
Escherichia coli, Haemophilus influenzae, and Helicobacter pylori 26695, among completed genomes.
The serum amyloid A (SAA) proteins comprise a family of vertebrate amphipathic α-helical apolipoproteins that associate predominantly with high density lipoproteins (HDL) [
,
]. They play a role in the mobilisation of cholesterol for tissue repair and regeneration []. The synthesis of these proteins is greatly increased (as much as a 1000 fold) in inflammation, being a major acute phase reactant together with C-reactive protein. They act as cytokine-like proteins that are involved in cell-cell communication and in inflammatory, immunologic, neoplastic and protective pathways []. Prolonged elevation of plasma SAA levels, as in chronic inflammation, results in a pathological condition, called amyloidosis, which affects the liver, kidney and spleen and which is characterised by the highly insoluble accumulation of SAA in these tissues. During chronic inflammation, SAA association with HDL can change its protein and lipid composition which abrogates the HDL anti-atherogenic properties, contributing to a pro-atherogenic state [,
].
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.The designation as "holocarboxylase synthetase"appears to be faulty. It originally comes from the annotation for the Triticum aestivum (Wheat) member, which notes similarity to human holocarboxylase synthetase. However, such similarity does not appear to exist.
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 archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes mammalian ribosomal protein L6 (L6 was previously known as TAX-responsive enhancer element binding protein 107); Caenorhabditis elegans ribosomal protein L6 (R151.3); Saccharomyces cerevisiae (Baker's yeast) ribosomal protein YL16A/YL16B; and Mesembryanthemum crystallinum (Common ice plant) ribosomal protein
YL16-like. These proteins have 175 (yeast) to 287 (mammalian) amino acids.
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 [
,
].L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding
site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of anancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites [
].
Glycosylphosphatidylinositol anchor biosynthesis protein Pig-F is involved in glycosylphosphatidylinositol (GPI) anchor biosynthesis [
,
,
]. This family also includes the Pif-F homologue GPI11 (glycosylphosphatidylinositol anchor biosynthesis protein 11) []. It is involved in the ethanolamine-phosphate transfer-step of GPI biosynthesis [].
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 L13 is one of the proteins from the large ribosomal subunit
[]. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol.
Aconitase/Iron-responsive element-binding protein 2
Type:
Family
Description:
Aconitase (aconitate hydratase;
) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [
,
]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is smaller than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) [].Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [,
]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated [
].IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [
,
]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.This entry represents Aconitate hydratase A [
] found predominantly in bacteria. Iron-responsive element-binding protein 2 [] and Cytoplasmic aconitate hydratase [] from animals; and Aconitate hydratase [] from plants also belong to this family.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This entry represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure [
].
Sft2 is a non-essential membrane protein that localizes to a late-Golgi compartment and is involved in vesicle fusion with the Golgi complex [
,
]. It is thought to interact with Sed5, a yeast t-SNARE protein that plays a role in ER-Golgi and intra-Golgi vesicular transport [,
]. Sft2 and related proteins are found in eukaryotes and show four putative transmembrane regions.
This domain is found in various proteins involved in cytochrome c
assembly from mitochondria, chloroplast and bacteria; including among others CycK from Rhizobium leguminosarum [], CcmC and CcmF from Escherichia coli [], CcsA from Chlamydomonas [], and orf240 from Triticum aestivum (wheat) mitochondria [].CcmC interacts directly with heme, and it is the only protein of the ccm operon that is strictly required for heme transfer [
]. CcmF contains a b-type heme and is thought to be a cytochrome c synthetase []. CcsA is required during biogenesis of c-type cytochromes at the step of heme attachment []. R. leguminosarum CycK and wheat orf240 also contain a putative heme-binding motif [,
].
This entry represents a group of plant serine/threonine protein phosphatases, including Arabidopsis BSU1 and BSU1-like proteins (BSLs) [
]. AtBSU1 is a phosphatase that acts as a positive regulator of brassinosteroid (BR) signalling [,
].This entry also includes putative serine/threonine-protein phosphatases from
Plasmodiumand green algae.
This entry represents proteins found in the N-terminal region of the essential protein Yae1. Proteins containing this domain include ORAOV1 (Oral cancer-overexpressed protein 1) and YAE1 [
]. Their function is not clear. In Saccharomyces cerevisiae, Lto1 (ORAOV1 homologue) forms a complex with Rli1 and Yae1, which relieves the toxic effects of reactive oxygen species (ROS) on biogenesis and function of the ribosome [].
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 S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [
], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian, plant, and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a β-α-β fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [].This entry represents bacterial, plastid and mitochondrial ribosomal S9 proteins. Mitochondrial ribosomal S9 is required for central cell maturation and endosperm development in
Arabidopsis thaliana[
].
This entry represents a group of arginine N-methyltransferases, including Skb1 from S. pombe [
], Hsl7 from S. cerevisiae [] and their homologues PRMT5 from animals [,
,
] and plants []. Skb1 is a mediator of hyperosmotic stress response in Schizosaccharomyces pombe []. Plant PMRT15 is involved in the post-transcriptional regulation of the circadian clock []. Human PRMT5 is a component of multiple protein complexes and contributes to essential cellular processes, such as RNA transport and splicing, cell cycle regulation, tumour growth, and chromatin remodelling, leading to either gene silencing or activation [].
This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
The microtubule organizing centres (MTOCs) of eukaryotic cells are the sites of nucleation of microtubules, and are known as the centrosome in animal cells and the spindle pole body in yeast. Gamma-tubulin, which is 30% identical to alpha and beta tubulins that form microtubules, appears to be a key protein involved in nucleation of microtubules.Gamma tubulin can assemble into complexes of various sizes with members of the GCP family. In budding yeast, the gamma tubulin-containing small complex (gammaTuSC) contains gamma tubulin, GCP2 and GCP3 (also known as Spc97 and Spc98). In Drosophila and vertebrates, gamma tubulin forms much larger assemblies, termed gamma-tubulin ring complexes (gammaTuRCs), with gamma tubulin, GCP2, GCP3, GCP4, GCP5 and GCP6. The purified gammaTuSC and gammaTuRC complexes exhibit a 'lock washer' shape [
]. However, the purified gammaTuSC has been shown to have a much lower microtubule-nucleating activity than intact gammaTuRC []. Several models have been proposed to explain their assembly and nucleation mechanism []. This entry represents the GCP family, whose members include GCP2/3/4/5/6 and Spc97/98 [
]. They contain the GRIP1 and GRIP2 motifs, which are predicted to participate in protein-protein interactions []. They are gamma tubulin binding proteins that have similar protein structures [].
This family, Ycf33, contains several plant, cyanobacterial and algal chlorplast encoded proteins of unknown function. The family is exclusively found in phototrophic organisms and may therefore play a role in photosynthesis.
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 S3 is one of the proteins from the small ribosomal subunit. In
Escherichia coli, S3 is known to be involved in the binding of initiator Met-tRNA. This family of ribosomal proteins includes S3 from bacteria, algae and plant chloroplast, cyanelle, archaebacteria, plant mitochondria, vertebrates, insects,
Caenorhabditis elegans and yeast []. This entry is the C-terminal domain.
Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. This family describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea.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 [
,
].
Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Atg proteins coordinate the formation of autophagosomes. The pre-autophagosomal structure contains at least five Atg proteins: Atg1p, Atg2p, Atg5p, Aut7p/Atg8p and Atg16p, found in the vacuole [
,
]. The C-terminal glycine of Atg12p is conjugated to a lysine residue of Atg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Autophagy protein 16 (Atg16) has been shown to bind to Atg5 and is required for the function of the Atg12p-Atg5p conjugate []. Autophagy protein 5 (Atg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [].This entry represents autophagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.
Coq4 is a component of a multi-subunit COQ enzyme complex, which plays a role in the coenzyme Q (ubiquinone) biosynthetic pathway [
,
,
]. In budding yeasts, Coq4 plays an essential role in organising the COQ enzyme complex and is required for steady-state levels of Coq3, Coq6, Coq7 and Coq9 [].
In Saccharomyces cerevisiae, Nucleolar complex protein 2 (Noc2) forms a nucleolar complex with Mak21 that binds to 90S and 66S pre-ribosomes. It also forms a nuclear complex with Noc3 that binds to 66S pre-ribosomes [
]. Both complexes mediate intranuclear transport of ribosomal precursors []. In humans, Noc2 (also known as NIR) acts as an inhibitor of histone acetyltransferase activity; prevents acetylation of all core histones by the EP300/p300 histone acetyltransferase at p53/TP53-regulated target promoters in a histone deacetylases (HDAC)-independent manner. It also acts as a transcription corepressor of p53/TP53- and TP63-mediated transactivation of the p21/CDKN1A promoter. It is involved in the regulation of p53/TP53-dependent apoptosis [
,
,
].Nucleolar complex-associated protein 2 (Noc2) from Arabidopsis thaliana appears to be involved in pre-ribosome export from the nucleus to the cytoplasm [
]. Also from A.thaliana, Protein REBELOTE influences floral meristem (FM) determinacy in an AGAMOUS and SUPERMAN-dependent manner, thus contributing to the floral developmental homeostasis [].
Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively [
].The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a β-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered.
This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes
affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high levelof UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for
the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand.
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 ofthe 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. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups bacterial, chloroplast, cyanelle, and most mitochondrial forms of ribosomal protein L11. L11 is a protein of 140 to 165 amino-acid residues. 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 bacterial, chloroplast and mitochondrial forms.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This family describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23.
The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, Vps23, Vps28, and Vps37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [
,
].
The elongation factor 4 (LepA or GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. LepA is a noncanonical GTPase that has an unknown function. It is highly conserved and present in bacteria, mitochondria, and chloroplasts [
]. LepA contains domains that are homologous to EF-G domain I, II, III, V. However, it also contains a C-terminal domain (CTD) that is not homologous to any region in EF-G. This entry represents the unique C-terminal region of LepA [
]. The CTD of LepA may play a primary role in back translocation by providing additional binding interactions with a back-translocated tRNA [].
Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The human Elongator six-subunit complex, known as holo-Elongator, has histone acetyltransferase activity directed against histone H3 and H4 [
,
]. It consists of two subcomplexes, a core subcomplex (ELP1-3), and an accessory subcomplex (ELP4-6) []. The elongator complex has been associated with many cellular activities, including transcriptional elongation [,
], but its main function is tRNA modification [,
]. It is required for the formation of 5-methoxy-carbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups on uridine nucleosides present at the wobble position of many tRNAs [
].This entry represents Elongator complex protein 6 (ELP6).
Nucleoporins (NUP) are the components of the nuclear pore complex (NPC). They can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. The nuclear pore complex constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. NPC is composed of at least 31 different subunits.This family includes nucleoporin Nup121 (Pom121) [
], Nup153 [] and Nup124 [] among others.
ArgJ (also known as Ornithine acetyltransferase/OAT) is a bifunctional protein that catalyses the first
and fifth steps
in arginine biosynthesis [
], coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in the arginine biosynthetic pathway. The structure has been determined for glutamate N-acetyltransferase 2 (ornithine acetyltransferase; ), an ArgJ-like protein from Streptomyces clavuligerus [
].Members of this family may experience feedback inhibition by L-arginine. The active enzyme is a heterotetramer of two alpha and two beta chains, where the alpha and beta chains are the result of autocatalytic cleavage. OATs found in the clavulanic acid biosynthesis gene cluster catalyze the fifth step only, and may utilize acetyl acceptors other than glutamate [
,
,
,
,
,
].
This serine-threonine protein kinase number 19 is expressed from the MHC and predominantly in the nucleus. Protein kinases are involved in signal transduction pathways and play fundamental roles in the regulation of cell functions. This is a novel Ser/Thr protein kinase, that has Mn2+-dependent protein kinase activity that phosphorylates alpha -casein at Ser/Thr residues and histone at Ser residues. It can be covalently modified by the reactive ATP analogue 5'-p-fluorosulphonylbenzoyladenosine in the absence of ATP, and this modification is prevented in the presence of 1 mM ATP, indicating that the kinase domain of is capable of binding ATP [
].
Protein in this entry are of unknown function and are found in cyanobacteria and the chloroplasts of algae. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA [
]. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [
] has revealed that S17 has virtually no groups exposed on the ribosomal surface.This entry represents ribosomal S17 proteins from bacteria and chloroplasts [
].
Urease is a nickel-binding enzyme that catalyses the hydrolysis of urea to form ammonia and carbamate. The activation of urease requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreG is a SIMIBI class GTPase that can be recruited by UreF-UreH complex [
].
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 L1 is the largest protein from the large ribosomal subunit. In Escherichia coli, L1 is known to bind to the 23S rRNA.
This model describe s bacterial and chloroplast ribosomal protein L1. Most mitochondrial L1 sequences are sufficiently divergent to be thecontained in a different entry (
).
Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product.PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [
,
,
]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants [
].This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (
) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [
].
This entry represents the PhzF family, which includes PhzF and uncharacterised isomerases. PhzF is part of the seven-gene operon phzABCDEFG, responsible for the synthesis of phenazine-1-carboxylic acid (PCA) in Pseudomonas species. PhzF is
a trans-2,3-dihydro-3-hydroxyanthranilate isomerase that catalyses the condensation of two molecules of trans-2,3-dihydro-3-hydroxyanthranilic acid (DHHA) into the phenazine ring system. The final product is not yet known [,
].
This family represents Ycf20, it is found in cyanobacteria and is also encoded in plant and algal chloroplasts; its function is unknown. As the family is exclusively found in phototrophic organisms it may therefore play a role in photosynthesis.
Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The human Elongator six-subunit complex, known as holo-Elongator, has histone acetyltransferase activity directed against histone H3 and H4 [
,
]. It consists of two subcomplexes, a core subcomplex (ELP1-3), and an accessory subcomplex (ELP4-6) []. The elongator complex has been associated with many cellular activities, including transcriptional elongation [,
], but its main function is tRNA modification [,
]. It is required for the formation of 5-methoxy-carbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups on uridine nucleosides present at the wobble position of many tRNAs [].This entry represents the ELP4 subunit. Mammalian ELP4 gene is implicated in rolandic epilepsy [
].
Antifreeze proteins (AFPs) are a class of proteins that are able to bind to and inhibit the growth of macromolecular ice, thereby permitting an organism to survive subzero temperatures by decreasing the probability of ice nucleation in their bodies [
]. These proteins have been characterised from a variety of organisms, including fish, plants, bacteria, fungi and arthropods. This entry represents insect AFPs of the type found in Tenebrio molitor iridescent virus and in Dendroides canadensis (Pyrochroid beetle).The structure of these AFPs consists of a right-handed β-helix with 12 residues per coil. The β-helices of insect AFPs present a highly rigid array of threonine residues and bound water molecules that can effectively mimic the ice lattice. As such, β-helical AFPs provide a more effective coverage of the ice surface compared to the α-helical fish AFPs [
].A second insect antifreeze from Choristoneura fumiferana (Spruce budworm) (
) also consists of β-helices, however in these proteins the helices form a left-handed twist; these proteins show no sequence homology to the current entry, but may act by a similar mechanism. The β-helix motif may be used as an AFP structural motif in non-homologous proteins from other (non-fish) organisms as well.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [
].
Peroxisomal membrane protein PEX14, or peroxin-14, is a core component of the peroxisomal translocation machinery or importomer [
,
]. PEX14 is involved in the docking of PEX5-bound protein onto the peroxisomal membrane, and it may be involved in the translocation step into the peroxisome matrix []. In addition to its role in protein docking, a role in transcriptional regulation has also been suggested for PEX14 [].
Mitochondrial functions rely on the correct transport of resident proteins
synthesized in the cytosol to mitochondria. Protein import into mitochondriais mediated by membrane protein complexes, protein translocators, in the outer
and inner mitochondrial membranes, in cooperation with their assistantproteins in the cytosol, intermembrane space and matrix. Proteins destined to
the mitochondrial matrix cross the outer membrane with the aid of the outermembrane translocator, the tOM40 complex, and then the inner membrane with the
aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat-shock protein 70 (mtHsp70), and translocase in the inner mitochondrial
membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC
and CXXC) of ~100 residues, which has been named DNL after a short C-terminalmotif of D(N/H)L [
,
,
].
This entry represents the conserved N-terminal domain of proteins that are involved in cell morphogenesis. Among these are furry proteins and homologues [
,
], and proteins PAG1 [] and Mor2 [].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].Ribosomal protein L9 is one of the proteins from the large ribosomal subunit.
In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongsto a family of ribosomal proteins grouped on the basis of sequence similarities [
].The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker [
]. Each domain contains an rRNA binding site, and the protein functions as astructural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an α-helix and a three-stranded mixed
parallel, anti-parallel β-sheet packed against the central α-helix. The long central α-helix is exposed to solvent in the middle and participates in thehydrophobic cores of the two domains at both ends.
This entry represents ribosomal L9 proteins found in bacteria and plastids, but not in mitochondria.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein L9 is one of the proteins from the large ribosomal subunit.
In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongsto a family of ribosomal proteins grouped on the basis of sequence similarities [
].The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker [
]. Each domain contains an rRNA binding site, and the protein functions as astructural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an α-helix and a three-stranded mixed
parallel, anti-parallel β-sheet packed against the central α-helix. The long central α-helix is exposed to solvent in the middle and participates in thehydrophobic cores of the two domains at both ends.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein L9 is one of the proteins from the large ribosomal subunit.
In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongsto a family of ribosomal proteins grouped on the basis of sequence similarities [
].The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker [
]. Each domain contains an rRNA binding site, and the protein functions as astructural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an α-helix and a three-stranded mixed
parallel, anti-parallel β-sheet packed against the central α-helix. The long central α-helix is exposed to solvent in the middle and participates in thehydrophobic cores of the two domains at both ends.
This entry represents Det1 family proteins [
]. Det1 (de-etiolated-1) is an essential negative regulator of plant light responses, and it is a component of the Arabidopsis CDD complex containing DDB1 and COP10 ubiquitin E2 variant. Mammalian Det1 forms stable DDD-E2 complexes, consisting of DDB1, DDA1 (DET1, DDB1 Associated 1), is a member of the UBE2E group of canonical ubiquitin conjugating enzymes and modulates Cul4A function [].
RNA-binding motif protein 8 (RBM8), also termed binder of OVCA1-1 (BOV-1) or RNA-binding protein Y14, is one of the components of the exon-exon junction complex (EJC) [
]. It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N terminus []. Three-dimensional modelling of the RBM8 RRM domain indicates that the sequences fold into an RNA-binding domain, forming a hydrophobic core between a β-sheet and two helices. The human RBM8A protein is ubiquitously expressed; the protein is localised predominantly in the cell nucleus and diffused throughout the cytoplasm []. It preferentially associates with mRNAs produced by splicing, including both nuclear mRNAs and newly exported cytoplasmic mRNAs. Evidence suggests the protein remains associated with spliced mRNAs as a tag to indicate the position of spliced introns. Human RBM8A protein specifically binds to MAGOH, the human homologue of Drosophila mago nashi, a protein required for normal germ plasm development in the Drosophila embryo []; a similar association occurs with the Drosophila RBM8 protein, Tsunagi []. The RBM8A and RBM8B protein sequences contain a putative bipartite nuclear localisation signal [
] at the N terminus, as well a stretch of glycine residues. In addition, the RRM contained within RBM8A and RBM8B contains one set of the two consensus nucleic acid-binding motifs, RNP-1 and RNP-2, characteristic of heterogeneous nuclear ribonucleoprotein (hnRNP).
This group represents eukaryotic protein phosphatase methylesterase 1. It demethylates proteins that have been reversibly carboxymethylated [
]. Carboxymethylation is a highly conserved means of regulation in eukaryotic cells.
COQ9 is an protein that is required for the biosynthesis of coenzyme Q [
], which functions in the respiratory electron transport chain and serves as a lipophilic antioxidant. In Saccharomyces cerevisiae (Baker's yeast), Q biosynthesis requires nine Coq proteins (Coq1-Coq9), with the COQ9 product acting subsequent to the prenylation of 4-hydroxybenzoic acid.
Homologous recombination is an evolutionarily conserved mechanism for the repair of double-strand breaks in DNA and the generation of genetic diversity. The primary function of homologous recombination in mitotic cells is to repair double-strand breaks or single-strand gaps that form as a result of replication fork collapse, from processing of spontaneous damage, and from exposure to DNA-damaging agents. During meiosis, homologous recombination is essential to establish a physical connection between homologous chromosomes to ensure their correct disjunction at the first meiotic division. In addition, the high frequency of meiotic recombination contributes to diversity by creating new linkage arrangements between genes, or parts of genes [
].The central step of homologous recombination is synapsis, the process of bringing together the two homologous strands. Rad51, a eukaryotic homologue of the prokaryotic recombinase RecA, mediates this process in eukaryotes [
]. Firstly a single-stranded DNA tail is coated by ATP-bound Rad51 to yield a nucleoprotein filament. This filament then searches for a homologous sequence within double-stranded DNA, and catalyses the exchange of strands between the single-stranded and double-stranded DNA substrates. The original broken end of the resulting branched DNA is now aligned with an appropriate matching sequence in an intact duplex, and is further processed by other enzymes [].Rad51 contains an N-terminal α-helical DNA binding domain not found in RecA, and a RecA-like C-terminal ATPase domain [
,
]. The active form of this protein is a long helical filament where the catalytically active unit is a homodimer [].
This group represents the cell division control protein Cdc6 and Cdc18, which are essential initiation factors for DNA replication [
].Cdc6 appears to have an important and perhaps unique dual role in S phase, it is first required for the initiation of DNA replication and then actively participates in the suppression of nuclear division. It interacts with the origin recognition complex (ORC). It targeted for degradation by the E3 ubiquitin ligase complex SCF (Cdc4) [
,
].Cdc18 is part of the checkpoint control that prevents mitosis from occurring until S phase is completed. It plays a key role in coupling S phase to start and mitosis. It acts at the initiation of DNA replication and plays a major role in controlling the onset of S-phase. Together with orp1, it is involved in the maintenance of replication forks and activation of cds1-dependent S-phase checkpoint [
,
,
,
,
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].The small subunits of bacterial and eukaryotic ribosomes have the same overall shapes (with structural elements described as head, body, platform, beak and shoulder). Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. [
]. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.
YLP motif-containing protein 1 plays a role in the reduction of telomerase activity during differentiation of embryonic stem cells by binding to the core promoter of TERT and controlling its down-regulation [
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This model finds eukaryotic ribosomal protein S9 as well as eukaryotic and archaeal ribosomal protein S4.
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 S4 is one of the proteins from the small ribosomal subunit. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is an insertion within
domain 1 and displays some structural homology with the ETS DNA binding domain [].This entry represents the domain found at the N terminus of small ribosomal subunits S4 and S9.
This N-terminal domain is found in Nucleolar protein 58/56 from fungi and animals and the homologues form plants. These are RNA-binding proteins of the NOP5 family [
]. Nop56 and Nop58 are components of box C/D small nucleolar ribonucleoprotein (snoRNP) particles [,
]. This domain interacts with Nop1 and forms the box B/C side, in the case of Nop56, or box C'/D side in the case of Nop58, of U3 snoRNP [].
This is a family of DNA-binding proteins, mainly found in bacteria and plants. Members of this family form homodimers which bind DNA via a tweezer-like structure [
,
,
,
]. The conformation of the DNA is changed when bound to these proteins []. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage []. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein.The crystal structure YbaB from Haemophilus influenzae revealed a core structure consisting of two layers, α/β; YbaB forms a tight dimer with a 3-layer structure, β/α/β [
].
This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [
].
This entry represents a domain found in C terminus of Atg11. Proteins containing this domain include Taf1 and Atg11. In Schizosaccharomyces pombe (fission yeast) Taf1 (taz1 interacting factor) is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) Atg11 is known to be involved in vacuolar targeting and peroxisome degradation [
,
].
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 [
,
].L35 is a basic protein of 60 to 70 amino-acid residues from the large subunit [
]. Like many basic polypeptides, L35 completely inhibits ornithine decarboxylase when present unbound in the cell, but the inhibitory function is abolished upon its incorporation into ribosomes []. It belongs to a family of ribosomal proteins, including L35 from bacteria, plant chloroplast, red algae chloroplasts and cyanelles. In plants it is a nuclear encoded gene product, which suggests a chloroplast-to-nucleus relocation during the evolution of higher plants [].
This family includes SRP-independent targeting protein 2 (SND2) from yeast and transmembrane protein 208 (TMEM208) from mammals. Both are localized to the endoplasmic reticulum (ER) [
,
]. SND2 works together with SND1 and SND3 in an alternative targeting route to the ER []. TMEM208 regulates both ER stress and autophagy [].SND2 was previously known as Env10 in Saccharomyces cerevisiae, and its homologue as Mug69 in Schizosaccharomyces pombe. They were identified as proteins involved in vacuolar processing and morphology [
] and meiosis [], respectively.
Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product.PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [
,
,
]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the D1 protein (also known as PsbA), which forms the reaction core of PSII as a heterodimer with the D2 protein. In higher plants, the N-terminal residues of both proteins, which are exposed to the stromal surface, can be reversibly phosphorylated. After insertion in the membrane, the C-terminal of the D1 protein is cleaved by a C-terminal processing protease to yield the mature protein [
]. This processing is essential for the assembly of a functional 4-atom manganese cluster, which involves binding to a highly conserved C-terminal alanine 344 []. The Mn cluster is located on the lumenal surface of the D1 and D2 proteins []. In addition to the Mn cluster, the D1/D2 core binds to a number of cofactors, including: two pheophytin molecules, only one of which is phytochemically active; non-haem iron; and two quinones, Qa (bound to D2) and Qb (bound to D1). Upon light excitation, an electron is transferred from the primary donor (chlorophyll a) via intermediate acceptor pheophytin to the primary quinone Qa, then to the secondary quinone Qb. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose.
Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S][
]. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S]form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins [
]. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen [].This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as
scaffolds [,
].
A variety of substrate carrier proteins that are involved in energy transfer
are found in the inner mitochondrial membrane [,
,
,
]. Such proteins include:ADP,ATP carrier protein (ADP/ATP translocase); 2-oxoglutarate/malate carrier
protein; phosphate carrier protein; tricarboxylate transport protein (orcitrate transport protein); Solute carrier family 25 member 16 (SLC25A16, also known as Graves disease carrier protein, GDC); yeast
mitochondrial proteins MRS3 and MRS4; yeast mitochondrial FAD carrier protein;and many others.
GDC, which belongs to the mitochondrial metabolite carrier family [
,
], is required for the accumulation of coenzyme A in the mitochondrial matrix []. The protein is recognised by IgGfrom patients with active Graves disease. It is an integral membrane protein thought to reside in the inner
mitochondrial membrane. The predicted amino acid sequence of 348 residuescomprises three similar domains.
Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component [
]. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) [
]. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers"in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion [
].SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologues of secA are also encoded in the chloroplast genome of some algae [
] as well as in the nuclear genome of plants []. It could be involved in the intraorganellar protein transport into thylakoids.
This is the conserved N-terminal of Syntaxin-18. Syntaxin-18 is found in the SNARE complex of the endoplasmic reticulum and functions in the trafficking between the ER intermediate compartment and the cis-Golgi vesicle. In particular, the N-terminal region is important for the formation of ER aggregates [
]. More specifically, syntaxin-18 is involved in endoplasmic reticulum-mediated phagocytosis, presumably by regulating the specific and direct fusion of the ER with the plasma or phagosomal membranes [].
In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity [
]. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of GS, thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed.P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein [
]. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome.
Other proteins highly similar to glnB are:Bacillus subtilis protein nrgB [
].Escherichia coli hypothetical protein ybaI [
].GlnK from Archaea and bacteria, an homologue of GlnB protein, which regulates ammonium transport (Amt) proteins [
,
]
