This entry represents protein LIN-9/ALWAYS EARLY (LIN-9/ALY). LIN-9 from Caenorhabditis elegans is a homologue of the Drosophila always early (ALY) protein, which functions as a repressor of cell cycle regulated genes [
,
].LIN-9 is a component of the evolutionary conserved DREAM (MuvB/DRM) complex, which represses transcription [
]. DREAM complex undergoes a cell cycle dependent switch of subunits. DREAM core binds to the E2F4 transcription factor and to the RBL2 (p130) in quiescent cells, while associates with the transcription factor B-MYB in the S-phase []. In humans, LIN-9 acts as a tumor suppressor and plays a role in the expression of genes required for the G1/S transition [,
]. In pluripotent embryonic stem cells (ESC), LIN-9 plays an important role for proliferation and genome stability by activating genes with important functions in mitosis and cytokinesis [].In Arabidopsis thaliana, ALY is expressed ubiquitously in vegetative and reproductive tissues [
].
This entry represents a group of uncharacterised plant proteins, including B3 domain-containing protein At2g31720 (also known as Protein AUXIN RESPONSE FACTOR 70) from Arabidopsis. These are DNA-binding proteins likely to be involved in stress response [
].
The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see
). Neither of the subunits shows sequence similarity to other filament-capping proteins [
].This entry represent the alpha subunit (CAPZA), which is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [
]. In Drosophila mutations in the alpha and beta subunits cause actin accumulation and subsequent retinal degeneration []. In humans CAPZA is part of the WASH complex that controls the fission of endosomes [].
This entry represents a group of eukaryotic and archaeal proteins. Eukaryotic members include EMC3, a subunit of the ER membrane protein complex (EMC) required for protein folding [
], and TMCO1, a ER calcium load-activated calcium channel []. Archaeal members may function as insertases of the archaeal plasma membrane [].
Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [
].
UVSSA is part of a UV-induced ubiquitinated protein complex involved in transcription-coupled nucleotide excision repair (TC-NER) in response to UV damage. It stabilise the TC-NER master organizing protein ERCC6 (also known as CSB) by delivering the deubiquitinating enzyme USP7 to TC-NER complexes [
].
This entry represents the N-terminal domain of the beta-catenin-like protein 1 (CTNNBL1). CTNNBL1 is a component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. In humans, it participates in AID/AICDA-mediated Ig class switching recombination (CSR) and may induce apoptosis [
,
].
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 L14 is one of the proteins from the large ribosomal subunit.
In bacteria, L14 is known to bind directly to the 23S rRNA. It belongs to afamily of ribosomal proteins which have been grouped on the basis of sequence
similarities.L14 is a protein of 119 to 137 amino-acid residues. This family distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
NDUFAF7 (NADH:ubiquinone oxidoreductase complex assembly factor 7), also known as MidA or mitochondrial protein midA homologue, plays a role in mitochondrial complex I activity [
].
This entry represents an ATPase that includes both a MinD-type, and FleN-type.MinD is a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE [
]. MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD []. Homologues can also be found in archaea, their exact role unknown.FleN is involved in the maintenance of flagellar number in Pseudomonas aeruginosa
. It has been shown to be an anti-activator against FleQ, an important transcriptional regulator of flagellar genes
.
This entry describes MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE [
]. MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD []. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate entry.
SPRING1 is a glycosylated Golgi-resident membrane protein involved in SREBP signaling and cholesterol metabolism. It modulates the proper localization of SCAP (SREBP cleavage-activating protein) to the endoplasmic reticulum, thereby controlling the level of functional SCAP [
].
This entry includes protein clueless from Drosophila, Clu1 from yeasts and protein CLU from plants. They are involved in proper cytoplasmic distribution of mitochondria [
,
].Protein clueless from Drosophila is required for mitochondrial subcellular localisation, interacts genetically with parkin [
]. It is highly expressed in larval neuroblasts, affects mitochondrial localisation and suppresses mitochondrial oxidative damage [].Budding yeast Clu1 is a subunit of the eukaryotic translation initiation factor 3 (eIF3). It can influence mitochondrial morphology and distribution [
]. Arabidopsis CLU, also known as FRIENDLY (At3g52140), is involved in regulating intermitochondrial association, a prelude to mitochondria fusion [
,
]. FRIENDLY may have expanded into a small gene family to help manage the energy metabolism of cells that contain both chloroplasts and mitochondria. These homologue are known as REDUCED CHLOROPLAST COVERAGE (REC) 1/2/3 (AT1G01320 , AT4G28080, AT1G15290). Together, they contribute to establishing the size of the chloroplast compartment [
].
This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [
].
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
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 a mitochondrial ribosomal subunit annotated as S27 in yeast and S33 in humans [
,
]. It is a small 106 residue protein. The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome [].
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 S10 consists of about 100 amino acid residues. In Escherichia coli, S10 is involved in binding tRNA to the ribosome, and also operates as a transcriptional elongation factor [
]. Experimental evidence [] has revealed that S10 has virtually no groups exposed on the ribosomal surface, and is one of the "split proteins": these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles. S10 belongs to a family of proteins [
] that includes: bacteria S10; algal chloroplast S10; cyanelle S10; archaebacterial S10; Marchantia polymorpha and Prototheca wickerhamii mitochondrial S10; Arabidopsis thaliana mitochondrial S10 (nuclear encoded); vertebrate S20; plant S20; and yeast URP2.
Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1. Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation [
], [].
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 L2 is one of the proteins from the large ribosomal subunit. The best conserved region is located in the C-terminal section of these proteins. In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups:Eubacterial L2.Algal and plant chloroplast L2.Cyanelle L2.Archaebacterial L2.Plant L2.Slime mold L2.Marchantia polymorpha mitochondrial L2.Paramecium tetraurelia mitochondrial L2.Fission yeast K5, K37 and KD4.Yeast YL6.Vertebrate L8.
This entry includes fungal chromatin modification-related protein Eaf7 and its mammalian homologue, MRG/MORF4L-binding protein (MRGBP). Eaf7/MRGBP is a component of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A [
].
This entry represents protein translocase subunit SecY.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 (SecY, 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 [
]. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The eubacterial secY protein [] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions. Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export [
]. Homologs of secY are found in archaebacteria []. SecY is also encoded in the chloroplast genome of some algae [] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.
Each of these transporters has ten alpha helical transmembrane segments [
]. The structure of a bacterial homologue of SLAC1 shows it to have a trimeric arrangement. The pore is composed of five helices with a conserved Phe residue involved in gating. One homologue, Mae1 from the yeast Schizosaccharomyces pombe, functions as a malate uptake transporter; another, Ssu1from Saccharomyces cerevisiae and other fungi including Aspergillus fumigatus, is characterised as a sulfite efflux pump; and TehA from Escherichia coli is identified as a tellurite resistance protein by virtue of its association in the tehA/tehB operon. In plants, homologues are found in the stomatal guard cells functioning as an anion-transporting pore []. Many homologues are incorrectly annotated as tellurite resistance or dicarboxylate transporter (TDT) proteins.
The budding yeast KRR1-interacting protein 1 (Kri1) is an essential nucleolar protein required for 40S ribosome biogenesis [
]. This entry also includes Kri1 homologues from animals and plants. Their function is not clear.
Ribosomal protein S12 is located at the interface of the large and small ribosomal subunits, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation [
]. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code [,
,
].This family consists of ribosomal protein S12 from bacteria, mitochondria, and chloroplasts.
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 bacterial and organellar branch of the ribosomal protein S7 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 [
,
].Ribosomal protein S11 [
] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. S14 is the eukaryotic homologue of S11; they constitute the uS11 family that includes bacterial, archaeal and eukaryotic proteins [
].This entry represents bacterial ribosomal S11 proteins, and also some (though not all) chloroplast and mitochondrial equivalents as well.
This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [
] and eukaryotic enzymes involved in biotin utilization [,
]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (
) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [
].
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 S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a β-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [
].This entry represents bacterial S13 and some, but not all instances of chloroplast and mitochondrial S13 as well.
Rev1 is a deoxycytidyl transferase involved in translesion DNA synthesis (TLS) pathway to bypass DNA lesions during replication [
]. During TLS, Y-family DNA polymerase (Poleta, Polkappa, Poliota and Rev1) incorporates a nucleotide opposite the DNA lesion, and then Polzeta (consitst of Rev3 and Rev7) carries out primer extension. Rev1 is a unique member of the Y polymerase family, since its catalytic activity is limited to DNA-dependent, deoxycytidyl transferase activity [,
,
].
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 describes the archaeal ribosomal protein and its equivalents in eukaryotes.
Coiled-coil domain-containing protein 86 (also known as Cyclon) is a cytokine-induced protein [
]. It has been shown to interact with hepatitis C virus (HCV) protein NS5A [].
Protein N-terminal asparagine amidohydrolase (NTAN1) acts on the side-chain deamidation of N-terminal asparagine residues to aspartate. It is required for the ubiquitin-dependent turnover of intracellular proteins that initiate with Met-Asn. These proteins are acetylated on the retained initiator methionine and can subsequently be modified by the removal of N-acetyl methionine by acylaminoacid hydrolase (AAH). Conversion of the resulting N-terminal asparagine to aspartate by PNAD renders the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule. NTAN1 does not act on substrates with internal or C-terminal asparagines and does not act on glutamine residues in any position [
,
].
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
This entry contains Serp1/Serp2 and yeast Ysy6 stress-associated endoplasmic reticulum proteins. In humans, Serp1 (also known as RAMP4) interacts with target proteins during their translocation into the lumen of the endoplasmic reticulum. It has also been shown to protect unfolded target proteins against degradation during ER stress. It may facilitate glycosylation of target proteins after termination of ER stress and may modulate the use of N-glycosylation sites on target proteins [
,
].
This domain of unknown function is found at the C-terminal of Protein NO VEIN from Arabidopsis, a protein essential for cell fate determination during embryogenesis [
]. It mediates this process through an auxin-dependent pathway []. It is also found in some restriction endonucleases.
This entry represents the C terminus (approximately 300 residues) of eukaryotic micro-fibrillar-associated protein 1, which is a component of elastin-associated microfibrils in the extracellular matrix [
].
This group represents peroxisome assembly protein 12, also known as Peroxin-12 or PEX12. PEX12 is required for protein import into peroxisomes [
,
,
].
Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defence against parasitic nucleic acids, and genome rearrangement. Many small regulatory RNAs are thought to function in nuclei, and in plants and fungi small interfering RNAs (siRNAs) associate with nascent transcripts and direct chromatin and/or DNA modifications. NRDE-2, is required for siRNA-mediated silencing in nuclei. NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNA interference, RNAi, the process whereby double-stranded RNA directs the sequence-specific degradation of mRNA [
].
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 protein L2 is found in all ribosomes and is one of the best conserved proteins of this mega-dalton complex. L2 is elongated, exposing one end of the protein to the surface of the intersubunit interface of the 50 S subunit and is essential for the association of the ribosomal subunits and might participate in the binding and translocation of the tRNAs [
]. This entry represents bacterial, chloroplast and mitochondrial forms.
This entry describes the riboflavin biosynthesis protein (ribD) as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region that is shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins that may be related to the riboflavin biosynthesis protein contain only the C-terminal domain.
This entry includes a group of meiosis specific proteins, including Spo22 from budding yeasts, ZIP4 from plants and TEX11 from mammals. They play an important role in normal crossover formation and meiotic chromosome segregation [
,
,
]. Impairment of these functions results in meiosis I (MI) segregation defect [].
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 L2 is one of the proteins from the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups:Eubacterial L2.Algal and plant chloroplast L2.Cyanelle L2.Archaebacterial L2.Plant L2.Slime mold L2.Marchantia polymorpha mitochondrial L2.Paramecium tetraurelia mitochondrial L2.Fission yeast K5, K37 and KD4.Yeast YL6.Vertebrate L8.This entry represents the ribosomal protein L2 from archaea. All members belong to the L2P family.
This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [
] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [,
,
].
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 L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
,
,
], groups:Eubacterial L5.Algal chloroplast L5.Cyanelle L5.Archaebacterial L5.Mammalian L11.Tetrahymena thermophila L21.Dictyostelium discoideum (Slime mold) L5Saccharomyces cerevisiae (Baker's yeast) L16 (39A).Plant mitochondrial L5.This entry represents the L5 protein in bacteria, chloroplasts and mitochondria.
TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription [
].
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 a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis [
]. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This entry represents the ribosomal protein L18 from bacteria and chloroplasts. The archaebacterial type is not included in this family.
Protein kinases (
) modify other proteins by chemically adding phosphate groups to them. This process is fundamental to most signalling and regulatory processes in the eukaryotic cell [
]. The protein kinases contain a catalytic core that is common to both serine/threonine and tyrosine protein kinases. The catalytic domain contains the nucleotide-binding site and the catalytic apparatus in an inter-lobe cleft. Structurally it shares functional and structural similarities with the ATP-grasp fold, which is found in enzymes that catalyse the formation of an amide bond. The three-dimensional fold of the protein kinase catalytic domain is similar to domains found in several other proteins. These include:the catalytic domain of phosphoinositide-3-kinase (PI3K), which phosphorylates phosphoinositides and, as such, is involved in a number of fundamental cellular processes such as apoptosis, proliferation, motility and adhesion [
] choline kinase, which catalyses the ATP-dependent phosphorylation of choline during the biosynthesis of phosphatidylcholine [
] 3',5'-aminoglycoside phosphotransferase type IIIa, a bacterial enzyme that confers resistance to a range of aminoglycoside antibiotics [
] This superfamily represents the protein-kinase domain and other related domains that share a similar structure.
This domain in found towards the C terminus in the Oval family of transcriptional repressors. These proteins are important regulators of growth and development in plants [
,
,
].
The light-harvesting complex (LHC) consists of chlorophylls A and B and the chlorophyll A-B binding protein. LHC functions as a light receptor that captures and delivers excitation energy to photosystems I and II with which it is closely associated. Under changing light conditions, the reversible phosphorylation of light harvesting chlorophyll a/b binding proteins (LHCII) represents a system for balancing the excitation energy between the two photosystems [
].The N terminus of the chlorophyll A-B binding protein extends into the stroma where it is involved with adhesion of granal membranes and photo-regulated by reversible phosphorylation of its threonine residues [
]. Both these processes are believed to mediate the distribution of excitation energy between photosystems I and II.This family also includes the photosystem II protein PsbS, which plays a role in energy-dependent quenching that increases thermal dissipation of excess absorbed light energy in the photosystem [
].
The serine incorporator/TMS membrane protein (TDE1/TMS) family include SERINC1-5 from mammals and membrane protein Tms1 from budding yeasts. Members in this family contain eleven transmembrane helices. SERINC1-5 function in incorporating serine into membranes and facilitating the synthesis of two serine-derived lipids, phosphatidylserine and sphingolipids [
]. Serinc3 (also known as TDE1) is overexpressed in tumours []. The function of Tms1 is not clear.
Dmc1 is a meiosis-specific RecA homologue [
]. It is a recombinase required for interhomologue recombination and double-strand break repair during meiosis [,
,
,
].
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 L3 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L3 is known to bind to the 23S rRNA and may participate in the formation of the peptidyltransferase centre of the ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities includes bacterial, red algal, cyanelle, mammalian, yeast and Arabidopsis thaliana L3 proteins; archaeal Haloarcula marismortui
HmaL3 (HL1), and yeast mitochondrial YmL9 [,
,
].This entry represents bacterial, mitochondrial and chloroplast L3 proteins. The organellar proteins typically contain a transit peptide sequence located N-terminal to the region covered by this entry.
This entry includes coiled-coil domain-containing protein 124 (Ccdc124) from animals and Oxs1 from fission yeasts. Ccdc124 is a centrosome and midbody protein involved in cytokinesis [
]. Oxs1 (SPBC29A10.12) is part of the Pap1-Oxs1 complex that regulates transcription when cells are exposed to diamide or Cd that causes disulfide stress [].
Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases (
). PP2C [
] is a monomeric enzyme of about 42kDa, that shows broad substrate specificity and is dependent on divalent cations (mainly manganese and magnesium) for its activity. The exact physiological role is still unclear. Three isozymes are currently known in mammals: PP2C-alpha, -beta and -gamma. In yeast, there are at least four PP2C homologues: phosphatase PTC1 [
] that have weak tyrosine phosphatase activity in addition to its activity on serines, phosphatases PTC2 and PTC3, and hypothetical protein YBR125c. Isozymes of PP2C are also known from Arabidopsis thaliana (Mouse-ear cress) (ABI1, PPH1), Caenorhabditis elegans (FEM-2, F42G9.1, T23F11.1), Leishmania chagasi and
Paramecium tetraurelia. In A. thaliana, the kinase associated protein phosphatase (KAPP)
[] is an enzyme that dephosphorylates the Ser/Thr receptor-like kinase RLK5 and contains a C-terminal PP2C domain.PP2C does not seem to be evolutionary related to the main family of serine/ threonine phosphatases: PP1, PP2A and PP2B. However, it is significantly similar to the catalytic subunit of pyruvate dehydrogenase phosphatase
() (PDPC) [
], which catalyzes dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. PDPC is a mitochondrial enzyme and, like PP2C, is magnesium-dependent.
This family consists of CASP and CASP-like proteins. In vascular plants Casparian strips span the cell wall of adjacent endodermal cells to form a tight junction that blocks extracellular diffusion [
]. Casparian Strip Membrane Domain Proteins (CASPs) are four-membrane-span proteins that recruit the lignin polymerisation machinery necessary for the deposition of Casparian strips in the endodermis. CASP-like proteins (CASPLs) are found in all major divisions of land plants as well as in green algae. In Arabidopsis, CASPLs show specific expression in a variety of cell types [].
A family containing a number of integral membrane proteins is named after TerC protein. TerC has been implicated in resistance to tellurium, and may be involved in efflux of tellurium ions. The tellurite-resistant Escherichia coli strain KL53 was found during testing of a group of clinical isolates for antibiotic and heavy metal ion resistance [
]. The determinant of the strain's tellurite resistance was located on a large conjugative plasmid, and analyses showed the genes terB, terC, terD and terE were essential for conservation of this resistance. Members of this family contain a number of conserved aspartates which may be involved in metal ion binding.A TerC homologue is known from the chloroplast thylakoid membrane from
Arabidopsiswhich is important for thylakoid membrane biogenesis in the developing chloroplast [
]; it is required for insertion of proteins into the thylakoid membrane [].
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 S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This family represents the eukaryotic and archaeal homologues of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes [
,
,
] and as either S12 or S23 in the Archaea [,
].S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding centre. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyses the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation [
,
]. S12 functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.
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 archaeal ribosomal proteins can be grouped on the basis of
sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 [
]. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have
233 to 264 amino acids.This entry represents the N-terminal region of these proteins.
This entry represents the N-terminal domain of tRNA modification GTPase MnmE (also known as TrmE) and similar proteins found in bacteria and eukaryotes. MnmE is a guanine nucleotide-binding protein involved in the modification of the wobble position of certain tRNAs that binds and hydrolyses GTP. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This domain consists of five β-strands and three α-helices and is necessary for mediating dimer formation within the protein. It is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate [
,
].
Proteins with a small GTP-binding domain include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors [
], tdhF, and many others []. In some proteins the domain occurs more than once. Among them there is a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST]motif (P-loop) by a long insert and are not easily detected by this model.
Survival protein SurE-like phosphatase/nucleotidase
Type:
Domain
Description:
This entry represents a SurE-like structural domain with a 3-layer alpha/bete/alpha topology that bears some topological similarity to the N-terminal domain of the glutaminase/asparaginase family. This domain is found in the stationary phase survival protein SurE, a metal ion-dependent phosphatase found in eubacteria, archaea and eukaryotes. In Escherichia coli,
SurE also has activity as a nucleotidase and exopolyphosphatase, and may be involved in the stress response []. E. coli cells with mutations in the surE gene survive poorly in stationary phase []. The structure of SurE homologues have been determined from Thermotoga maritima [] and the archaea Pyrobaculum aerophilum []. The T. maritima SurE homologue has phosphatase activity that is inhibited by vanadate or tungstate, both of which bind adjacent to the divalent metal ion.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This entry represents the ribosomal protein of the eukaryotic cytosol that is homologous to S2 of bacteria. It is designated typically as SA in eukaryotes. The protein is required for the assembly and/or stability of the 40S ribosomal subunit and required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits [
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This family describes the ribosomal protein of the eukaryotic cytosol and of archaea, homologous to S2 of bacteria. It is designated typically as SA in eukaryotes and SA or S2 in the archaea.
This domain can be found in bacterial, plant and other metazoa transmembrane proteins. Many of the members are multi-pass transmembrane proteins. This domain represents the N-terminal region which contains a conserved homology domain (CHD1) [
].
Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species [
,
,
]. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components []. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and P2B, which form P1A/P2B and P1B/P2A heterodimers []. Some plants have a third P-protein, called P3, which is not homologous to P1 and P 2 [].In humans, P1 and P2 are strongly autoimmunogenic. They play a significant role in the etiology and pathogenesis of systemic lupus erythema (SLE). In addition, the ribosome-inactivating protein trichosanthin (TCS) interacts with human P0, P1, and P2, with its primary binding site in the C-terminal region of P2. TCS inactivates the ribosome by depurinating a specific adenine in the sarcin-ricin loop of 28S rRNA [
].Archaeal L12 is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12 is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative [
].This entry includes eukaryotic 60S acidic ribosomal protein P1/P2 , as well as archaeal 50S ribosomal protein L12. These proteins play an important role in the elongation step of protein synthesis [
,
].
Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase;
) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [,
]. The PTP superfamily can be divided into four subfamilies []:(1) pTyr-specific phosphatases(2) dual specificity phosphatases (dTyr and dSer/dThr)(3) Cdc25 phosphatases (dTyr and/or dThr)(4) LMW (low molecular weight) phosphatasesBased on their cellular localisation, PTPases are also classified as:Receptor-like, which are transmembrane receptors that contain PTPase domains [
]
Non-receptor (intracellular) PTPases [
]
All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel β-sheet with flanking α-helices containing a β-loop-α-loop that encompasses the PTP signature motif [
]. Functional diversity between PTPases is endowed by regulatory domains and subunits. Tyrosine specific protein phosphatases (PTPases) contain two conserved cysteines, the second one has been shown to be absolutely required for activity. This entry represents the PTPase domain that centre on the active site cysteine. A number of conserved residues in its immediate vicinity have also been shown to be important.
In Saccharomyces cerevisiae, Noc4 is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. It forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits [
,
,
].
This entry includes budding yeast Sit4-associated proteins, such as Sap155, Sap185, and Sap190. Sit4 is a phosphatase involved in a variety of processes including transcription, translation, bud formation, glycogen metabolism, monovalent ion homeostasis, H+ transport, and telomere function [
]. This entry also includes mammalian PP6 (Sit4 homologue)-associated proteins, such as PP6R1, PP6R2, and PP6R3 [
]. They are regulatory subunits of PP6 involved in the PP6-mediated dephosphorylation of NFKBIE opposing its degradation in response to TNF-alpha [].
Proteins containing this domain include ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins [
]. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins.The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved [
]. It consists of a three-stranded β-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis [].
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 N-terminal domain appears to be specific to the eukaryotic ribosomal proteins L25, L23, and L23a.
This entry represents the N-terminal domain of kinetochore protein Nuf2, which is part of the Ndc80 complex. This domain fold as a CH domain consisting of a four-helix bundle containing the parallel helices alphaA, alphaC, alphaE, and alphaG, similar to that in Ndc80. These CH domains from Nuf2 and Ndc80 forms the globular rod at one end the complex [
,
]. The ability of the Ndc80 complex to bind microtubules resides on the tightly packed CH domains from Nuf2 and Ndc80 []. This complex binds to the spindle and is required for chromosome segregation and spindle checkpoint activity [,
,
,
,
,
,
].
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 ribosomal protein L15 and homologues found in bacteria, chloroplasts and mitochondria.
This entry includes coiled-coil domain-containing proteins 90 (CCDC90) and related proteins. CCDC90A is a key regulator of the mitochondrial calcium uniporter (MCU) and hence was renamed MCUR1 [
,
,
]. A study in mammals and in yeast homologue fmp32 has reported that MCUR1 is a cytochrome c oxidase assembly factor and that it has an indirect role as a regulator of MCU [], however, subsequent publications confirmed the function of MCUR1 as a regulator of MCU [,
]. The role of CCDC90B proteins is still not known.
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 5 (ELP5).
In general, proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR) [
,
]. These proteins mediate resistance to a wide range of cationic dyes, fluroquinolones, aminoglycosides and other structurally diverse antibodies and drugs. MATE proteins are found in bacteria, archaea and eukaryotes. These proteins are predicted to have 12 α-helical transmembrane regions, some of the animal proteins may have an additional C-terminal helix [].
In bacteria, FtsZ [
,
,
,
] is an essential cell division protein involved in the initiation of this event. It assembles into a cytokinetic ring on the inner surface of the cytoplasmic membrane at the place where division will occur. The ring serves as a scaffold that is disassembled when septation is completed. FtsZ ring formation is initiated at a single site on one side of the bacterium and appears to grow bidirectionally. In Escherichia coli, MinCD , encoded by the MinB locus, form a complex which appears to block the formation of FtsZ rings at the cell poles, at the ancient mid cell division sites, whilst MinE, encoded at the same locus, specifically prevents the action of MinCD at mid cell.
FtsZ is a GTP binding protein with a GTPase activity. It undergoes GTP-dependent polymerisation into filaments (or tubules) that seem to form a cytoskeleton involved in septum synthesis. The structure and the properties of FtsZ clearly provide it with the capacity for the cytoskeletal, perhaps motor role, necessary for "contraction"along the division plane. In addition, however, the FtsZ ring structure provides the framework for the recruitment or assembly of the ten or so membrane and cytoplasmic proteins, uniquely required for cell division in E. coli or Bacillus subtilis, some of which are required for biogenesis of the new hemispherical poles of the two daughter cells. FtsZ can polymerise into various structures, for example a single linear polymer of FtsZ monomers, called a protofilament. Protofilaments can associate laterally to form pairs (sometimes called thick filaments), bundles (ill-defined linear associations of multiple protofilaments) or thick filaments, sheets (parallel or anti-parallel two-dimensional associations of thick filaments) and tubes (anti-parallel associations of thick filaments in a circular fashion to form a tubular structure). In addition, small circles of FtsZ monomers (a short protofilament bent around to join itself, apparently head to tail) have been observed and termed mini-rings. FtsZ is a protein of about 400 residues which is well conserved across bacterial species and which is also present in the chloroplast of plants [
] as well as in archaebacteria []. FtsZ is a homologue of eukaryotic tubulin with which it shows structural similarity.
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 L26 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. Eukaryotic L26 is a conserved protein that shares notable sequence and structure identity with archaeal and eubacterial L24. This entry represents the archaeal L24 and eukaryotic branch of these proteins.
Queuosine salvage proteins occur in most Eukarya as well as in a few bacteria possible via horizontal gene-transfer. Queuosine (Q) is a chemical modification found at the wobble position of tRNAs that have GUN anticodons, and it ensures faithful translation of the respective C- and U-ending codons. Most bacteria synthesize queuosine de novo, whereas eukaryotes rely solely on salvaging this essential component from the environment or the gut flora. This entry represents queuosine salvage proteins (Qng1, also known as DUF2419) which have been identified as a queuosine nucleoside glycosylases that play an essential role in allowing eukaryotic cells to salvage Q from bacterial sources and to recycle Q from endogenous tRNAs [
,
].
This entry represents proteins found in plants, lower eukaryotes, and bacteria and the chloroplast where it is annotated as Ycf49 or Ycf49-like. The function is not known though several members are annotated as putative membrane proteins. As the family is primarily found in phototrophic organisms it may 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 [,
].This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [
].
Rrp15 is a constituent of pre-60S ribosomal particles. It is required for large subunit rRNA maturation, in particular processing of the 27S pre-rRNA at the A3 and B1 sites to yield 5.8S and 25S rRNA [
].
A number of autophagy-related proteins have been identified in yeast, including the key autophagic protein Atg8, which is a ubiquitin-like protein with a structure consisting of two amino-terminal α-helices and a ubiquitin-like core [
,
]. Many other eukaryotes contain multiple Atg8 orthologues. Atg8 genes of multicellular animals can be divided into three subfamilies: microtubule-associated protein 1 light chain 3 (MAP1LC3 or LC3) [], gamma-aminobutyric acid receptor-associated protein (GABARAP) and Golgi-associated ATPase enhancer of 16kDa (GATE-16) [,
]. Family members are involved in diverse intracellular trafficking and autophagy processes.
The Histidine Triad (HIT) motif, His-x-His-x-His-x-x (x, a
hydrophobic amino acid) was identified as being highly conserved in a variety of organisms [,
]. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the FHIT branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases [,
]. In budding yeast Hnt1 has been shown to have adenosine monophosphoramidase activity and function as positive regulators of Cdk7/Kin28 in vivo [
,
]. FHIT plays a very important role in the development of tumours. In fact, FHIT deletions are among the earliest and most frequent genetic alterations in the development of tumours [,
]. The third branch of the HIT superfamily, which includes GalT homologues, contains a related His-X-His-X-Gln motif and transfers nucleoside monophosphate moieties to phosphorylated second substrates ratherthan hydrolysing them [
].
Chaperone DnaJ was originally characterised from Escherichia coli as a 41kDa heat shock protein. DnaJ has a modular structure consisting of a J-domain, a proximal G/F-domain, and a distal zinc finger domain, followed by less conserved C-terminal sequences. Since then, a large number of DnaJ-related proteins containing a J-domain have been characterised from a variety of different organisms. In the genome of Arabidopsis thaliana a total of 89 J-domain proteins have been identified [
].This entry represents a C-terminal domain found in some eukaryotic DnaJ-like proteins, including member 11 from the subfamily C1 and protein DnaJ 13 from Arabidopsis. DNAJC11 is a mitochondrial outer membrane protein involved in mitochondrial biogenesis and in the response to microenvironment changes and requirements. The J-domain mediates its mitochondrial localization, while this domain is critical for protein-protein interactions [
].
This entry represents the N-terminal domain of autophagy-related protein 13 (Atg13) from yeasts, animals and plants. They function in autophagy.Fission yeast autophagy initiation is controlled by the Atg1 kinase complex, which is composed of the Ser/Thr kinase Atg1, the adaptor protein Atg13, and the ternary complex of Atg17-Atg31-Atg29. Atg13 recruits Atg1 to the site of autophagosome formation and enhancing Atg1 kinase activity. Atg13 may have additional functions that are independent of a direct interaction or permanent colocalization with Atg1 [
]. In vertebrates, the orthologous ULK1 kinase complex contains the Ser/Thr kinase ULK1 and the accessory proteins ATG13, RB1CC1, and ATG101 [
]. Through its regulation of ULK1 activity, Atg13 plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation [].
This family of plant proteins represent Ycf58 a chloroplast encoded protein that is restricted to the monocots and conifers. The proteins have no known function but as the family is exclusively found in the chloroplasts of phototrophic organisms it may play a role in photosynthesis.
Fe/S biogenesis protein NfuA is involved in iron-sulphur cluster biogenesis under severe conditions such as iron starvation or oxidative stress. It binds a 4Fe-4S cluster and can transfer this cluster to apoproteins, thereby intervening in the maturation of Fe/S proteins. This protein could also act as a scaffold/chaperone for damaged Fe/S proteins. Fe/S biogenesis protein NfuA is required for Escherichia coli to sustain oxidative stress and iron starvation, it is also necessary for the use of extracellular DNA as the sole source of carbon and energy.
Queuosine biosynthesis protein (QueC), also known as 7-cyano-7-deazaguanine synthase, catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ0) [
,
,
].
The function of this family of proteins is not known. A member of this family, YicR, formerly called RadC [
], is a putative JAMM-family deubiquitinating enzyme [].
NadR functions as a transcriptional regulator in Salmonella enterica [
]. When NAD+ is available, NadR is bound with its corepressor, NAD+, and this leads to DNA binding activity that acts as a repressor for several genes needed for de novo NAD+ biosynthesis [,
]. NadR also possesses both NMN adenylyltransferase (NMNAT) and nicotinamide ribonucleoside kinase (RNK) activity []. Haemophilus influenzae lacks de novo biosynthetic pathways for NAD+ and also lacks a helix-turn-helix DNA binding domain present in NadR of S. enterica. H. influenzae NadR does not function as a repressor, but has enzymatic activity. Nicotinamide riboside (NR) enters the NAD+ resynthesis pathway after uptake, it is phosphorylated to obtain NMN by a nicotinamide RNK activity, and subsequently, NAD+ is synthesized from NMN and ATP via an NMNAT activity [
]. NadR is a multifunctional biosynthesis/regulator protein.
The CorA transport system is a primary Mg2+ transporter for Bacteria and Archaea. Some members in this family may have a function other than Mg2+ transport [
]. Prokaryotic CorA can be classified into two sub-groups: (1) T. maritima type (group A) (2) E. coli and S.typhimurium type (group B) []. Thermotoga maritima CorA (TmCorA) has been reported to be an efflux system. It only has 2 transmembrane (TM) domains,TM1 and TM2 [
,
,
]. The loop connecting TM1 and TM2 contains the conserved CorA signature motifs YGMNF and MPEL. With its N- and C-terminal ends face the cytosol and its similarity to the class II CorA (a CorA group lacking the MPEL motif and may transport divalent cations out of the cell), TmCorA is predicted to be primarily involved in ion efflux []. It forms a pentameric membrane protein channel featuring a possible ion discriminating aspartate ring at the cytoplasmic entrance of the pore and two distinct cytoplasmic metal binding sites per monomer, which could have regulatory roles [,
]. E. coli and S.typhimurium CorA was predicted to have an unusual membrane topology with a relatively large N-terminal periplasmic domain (CorA-PPD) followed by a compact C-terminal domain forming three transmembrane (TM1-3) segments [
,
]. However, a suggestion that TM1 is not completely transmembrane but rather peripheral to the membrane has been proposed, and in this scenario both terminalswould face the same side. A high-resolution structure from this group of proteins is needed to clarify this [
].
