This entry represents a group of mitochondrial carrier proteins, including Mtm1 from budding yeasts and SLC25A39/40 from humans. Mtm1 is a
pyridoxal 5'-phosphate (PLP) transporter and is involved in mitochondrial iron homeostasis []. SLC25A39 and its paralogue SLC25A40 are mitochondrial transporters essential for glutathione import into mitochondria, which is required for the activity and stability of proteins containing iron-sulfur clusters, as well as erythropoiesis []. Knockdown of SLC25A39 in a zebrafish model has been shown to disrupt heme biosynthesis and results in profound anemia [].
Protein methyltransferase CheR binds to a specific sequence at the C-termini of some chemotaxis receptors and from this tethering position methylates neighbouring receptor molecules [
].
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 archaeal S7 ribosomal proteins.
Virtually all mitochondrial precursors are imported via the same
mechanism []: precursors first bind to receptors on the mitochondrialsurface, then insert into the translocation channel in the outer membrane.
Many outer-membrane proteins participate in the early stages of import,four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor.
MAS20, which forms a subcomplex with MAS22, seems to interact with most orall mitochondrial precursors, suggesting that the protein binds directly
to mitochondrial targeting sequences. The MAS37 and MAS70 components alsoform a subcomplex, the two subcomplexes possibly binding via their trans-
membrane (TM) regions - the TM region of MAS70 promotes oligomerisationof attatched protein domains and shares sequence similarity with the
TM region of MAS20 [].MAS20 is also known as TOM20.
MAP1-family proteins are microtubule-associated proteins (MAPs) that bind along the microtubule lattice. Mammalian genomes usually contain three family members, MAP1A, MAP1B and MAP1S. Only one family member, Futsch, is found in Drosophila.Human MAP1A and MAP1B, are predominantly expressed in neurons, where they are thought to be important in the formation and development of axons and dendrites [
]. Human MAP1A and MAP1B stabilise microtubules and interact with other cellular components, including filamentous actin and signaling proteins. The activity of MAP1A and MAP1B is controlled by upstream signaling mechanisms, including the MAP kinase and glycogen synthase kinase-3 beta pathways []. Human MAP1S is a heterodimer with a heavy and a light chain. Both MAP1S heavy and light chains interact with microtubules, while MAP1S light chain interacts with actin [
]. MAP1S is involved in the formation of microtubule bundles []. It mediates aggregation of mitochondria resulting in cell death and genomic destruction (MAGD) []. It bridges autophagic components with microtubules and mitochondria plays a role in apoptosis [,
,
].
Cerebellar degeneration-related protein 2 is a tumour antigen, which is aberrantly expressed in breast and ovarian tumors [
]. It is also an important tumor antigen for papillary renal cell carcinoma [].
This entry represents penicillin-binding protein activator LpoB. It has been suggested that penicillin-binding protein activator LpoB acts as a regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1B (PBP1b) [,
].
Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria) [
]. This protein is cross-linked by a spore coat-associated transglutaminase.
This family includes the Alkaline phosphatase-like protein PglZ from Bacillus cereus and Escherichia coli, putative phosphatases and core proteins of a type 1 BREX system. BREX systems (bacteriophage exclusion) provide immunity against bacteriophage. This system allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA. Methylation of bacterial DNA by PglX probably guides self/non-self discrimination [
,
].
Seminal vesicle protein I (SVP-1) is one of the four major secretory proteins secreted by Cavia porcellus (Guinea pig) seminal vesicle epithelium. It is a clotting protein that serves as the substrate in the formation of the copulatory plug. Covalent clotting of this protein is catalyzed by a transglutaminase and involves the formation of gamma-glutamyl-epsilon-lysine crosslinks. SVP-1 sequence contains eight repeats of a twenty four amino acid residue domain. There are seven invariant residues in these repeats, three of them (two lysines and one glutamine) probably participate in the cross-links [
].These repeats are also present twice in the N-terminal region of the precursor of human skin elafin, an inhibitor of elastase as well as in the precursor of Sus scrofa (Pig) sodium/potassium atpase inhibitor SPAI-2.
Budding yeast nucleolar complex-associated protein 3 (Noc3) is required for initiation of DNA replication and for synthesis of 60S ribosomal subunits and the transport of pre-ribosomes from the nucleoplasm to the cytoplasm [
,
]. This entry also includes Noc3 homologues from animals and plants. The mammalian Noc3 is a positive regulator in adipocyte differentiation [].
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.
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.
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.
The bacterial S-layer forms a regular structure, composed of a monolayer of one glycolprotein on the surfaces of many prokaryotic species. S-layers fulfil different functions, such as serving as attachment structures for extracellular enzymes and acting as major virulence determinants for pathogenic species.This entry represents a family of S-layer proteins from Lactobacillus [
].
Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein (NSs). The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase.This entry represents the segment S non-structural protein, NSs. This protein is present in infected cells, but absent from purified virus particles [
,
]. It is not essential for virus replication, but contributes substantially to pathogenesis []. This may be due to the capacity of NSs to interfere with the host immune response; it has been shown to inhibit the production of alpha/beta interferons, and to inhibit interferon regulatory factor-mediated cell death [,
]. Studies indicate that NSs suppresses host mRNA synthesis by sequestering subunits of the basal transcription factor TFIIH, explaining the dramatic drop in RNA synthesis observed upon infection [].
Adenoviruses encode a highly basic protein called protein VII that resembles cellular histones. Protein VII forms complexes with nucleosomes, limiting DNA accessibility, and sequesters protein HMGB1 in the chromatin. HMGB1 is normally released in response to inflammatory stimuli and mediates activation of immune responses. This is thought to be part of a viral strategy to control extracellular immune signaling [
]. Protein VII also plays a role in packaging the viral DNA [].
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.
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.
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.
The phenazine biosynthesis proteins A and B are involved in the biosynthesis of this antibiotic. Phenazine is a nitrogen-containing heterocyclic molecule with important implications in virulence, competition and biological control [
].
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.
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.
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.
Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions [].The comG operon of Bacillus subtilis encodes seven membrane associated proteins which function in binding of transforming DNA to the competent cell surface [
]. ComGC, GD, GE and GG have N-terminal sequence motifs typical of type 4 pre-pilins and are processed by a pathway that requires the product of comC, also an essential competence gene. They form pilin-like structures that are localised to the cytoplasmic membrane and cell wall []. The comG operon also consist of ComGF, a small integral membrane protein, ComGA and ComGB, which are predicted to be a nucleotide binding protein and an integral membrane protein respectively []. When strains missing each of the 7 proteins are created, they were all found to be nontransformable and failed to bind transforming DNA to the cell surface []. This family represents pseudopilin ComGC.
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 represents a family of uncharacterised conserved proteins mainly found in Gammaproteobacteria, including Uncharacterized protein YjcB from Escherichia coli (
).
This family is the major core protein 4b. It is a major component of the virion core that undergoes proteolytic processing during the immature virion (IV) to mature virion (MV) transition. It is essential for the formation of a structurally normal core [
,
].
This family of proteins is functionally uncharacterised. Some family members have been annotated as being involved in signal transduction, on the basis they possess a DICT domain (
). However, there is no experimental evidence to support this function, and the DICT domain's suggested role in sensory function in highly speculative.
This entry represents a protein family found in bacteria and archaea, almost always in the same genomes as members of family
, and frequently as a nearby gene. The few invariant residues in this family, found toward the N terminus, include a dipeptide DE, a tripeptide HGP, and two different Arg residues. Up to three members may be found in a genome.
This group of proteins include the probable dolichyl-phosphate-hexose flippase Agl23 (
) from the extremely halophilic archaea Haloarcula hispanica. This protein may be involved in both N- and O-glycosylation of S-layer glycoproteins [
].
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.
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, these proteins are predicted integral membrane proteins (with several transmembrane segments), and are present in an operon with a predicted multidrug efflux pump.
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 represents a family of bacterial uncharacterised proteins that includes PA2169 from Pseudomonas aeruginosa (
). This protein shows a ferritin-like topology with a four-helix-bundle fold that lacks metal-ion-binding site typical of the ferritin family but has a potential metal-binding site [
]. Its function is still unknown.
This entry represents a family of uncharacterised proteins predominantly found in bacteria that includes DUF2383 domain-containing protein from Pseudomonas aeruginosa (
). This protein shows a ferritin-like topology with a four-helix-bundle fold that lacks metal-ion-binding site typical of the ferritin family but has a potential metal-binding site [
]. Its function is still unknown.
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.
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 represents a family of fungal 37S mitochondrial ribosomal S25 proteins which are a component of the mitochondrial small ribosomal subunit [
].
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.
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.
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 family includes several proteins of unknown function. Members of this family may be involved in nitrogen fixation, since they are found within nitrogen fixation operons.
This family consists of IpgB1 and IpgB2 from Shigella [
] as well as related proteins TrcA, Map, EspM from Escherichia coli. Members of this family seem to be involved in pathogenicity and have been identified as small GTPases mimicking or activating proteins [,
].
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.
Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La. The La protein is a 47kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome [
]. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor []. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation []. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis []. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif [].Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [
].
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.
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.
Bacterial magnetosomes are intracellular membrane-enclosed, nanosized magnetic crystals. Mms48, along with the three other genes in the same operon, appear to influence magnetosome size and number [
].
There is currently no experimental data for members of this group or their homologues. Though they contain a version of the type II restriction endonuclease domain, it lacks the signature P[D]-[D/E]-X-K. It is therefore not clear if members of this group are enzymatically active endonucleases.
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.
Eosinophil granule major basic protein (MBP) is a low molecular weight
cationic protein present in the crystalloid core of the eosinophil granule[
]. It is a potent toxin for helminths and mammalian cells, and may have important roles in allergic and inflammatory reactions, it can release histamine from mast cells and damage epithelial cells of bronchial tubes.MBP is also involved in antiparasitic defence mechanisms and immune hypersensitivity reactions. The protein is a single arginine-rich polypeptide[
], its pro-portion being rich in glutamic and aspartic acids. It has been suggested that the protein is translated as a nontoxic precursor that protects the eosinophil from damage while it is processed through the endoplasmic reticulum to its sequestered site in the granule core toxic MBP []. The sequence of MBP has been shown to contain a C-type lectin (CTL) domain []. CTL domains are 110-130 residue motifs that appear to function as calcium-dependent carbohydrate-recognition domains [,
,
].
Members of this protein family are EutC, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine) [
], Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. This family belongs to the ornithine cyclodeaminase/mu-crystallin family ().
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.
EutD is known as DoeA in Halomonas elongata. DoeA is involved in the ectoine degradation pathway where it hydrolyses ectoine to alpha-N-acetyl diaminobutyric acid [
].
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.
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.
Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include include Rhizobium loti (Mesorhizobium loti), Silicibacter pomeroyi and Sinorhizobium meliloti 1021, where it is known to be induced by ectoine. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.,
Members of this entry are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Rhizobium loti (Mesorhizobium loti), Silicibacter pomeroyi, Agrobacterium tumefaciens, Pseudomonas putida and Sinorhizobium meliloti 1021, where it is known to be induced by ectoine. Members resemble threonine dehydratases.
Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions [
].These proteins are part of a set in Streptococcus pneumoniae that undergo late induction by competence pheromone [
]. There is currently no data that address the function, nor is it known if induction occurs in other species. However, the proteins are predicted to be integral membrane proteins (with several transmembrane segments).
Proteins in this family are a component of the helicase/primase complex. The helicase generates single stranded DNA by unwinding the double helix at the replication forks, and the primase synthesizes short RNA primers that the polymerase then elongates [
]. The function of the proteins, which have no known catalytic activity, is unknown, but they have been shown to be distantly related to B-family polymerases with a substantial reduction in nucleotide binding sites and loss of the active site [].
This entry represents SYS1 homologues (hSYS1). hSYS1 is a multi-pass membrane protein found in the Golgi apparatus membrane. hSYS1 appears to be involved in protein trafficking and may serve as a receptor for ARFRP1 (Arf-related protein 1), the human homologues of Arl3p [
]. Arf family members are GTPases that are crucial for the organisation of membrane traffic. They act by recruiting coat proteins to form transport vesicles, and motor proteins to move both transport carriers and organelles []. Arfs can also carry lipid modifications that are involved in membrane recruitment. The function of hSYS1 is unknown, but it controls the location of ARFRP1, apparently by forming a complex with the protein, and could therefore function in the Arl3p/Arl1p pathway.
Members of this protein family have an N-terminal radical SAM domain and a C-terminal domain whose function is unknown (see
). The C-terminal region has several conserved Cys residues, one of which is replaced by selenocysteine in at least five bacterial reference genomes.
Members of this protein family average 125 in length, roughly half of which is the repetitive and extremely Gly-rich C-terminal region. Virtually all members occur in the Cyanobacteria, in a neighbourhood that includes a radical SAM/SPASM domain, often a marker of peptide modification systems.
A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homologue, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Members of this family are designated ScmC.
A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homologue, and a conserved hypothetical protein [
]. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Members of this family are the PqqD-like protein.
Members of this uncharacterised protein family are found broadly but sporadically among bacteria and archaea, including members of the genera Mycobacterium, Nostoc, Acinetobacter, Planctomyces, Geobacter, Streptomyces, Methanospirillum, etc. Their function is unknown.
Representatives of this family include a 13-member paralogous family of proteins about 215 amino acids in length from the termite gut bacterium Opitutaceae bacterium TAV2, a member of the Verrucomicrobia. Family members contain an N-terminal signal peptide and a C-terminal PEP-CTERM putative protein sorting signal. Conserved residues such as an invariant Arg and a lack of conspicuous low-complexity sequence suggest a globular structure and possible enzymatic activity. Members average about thirty percent sequence identify overall, but over seventy percent in the PEP-CTERM region. The function of this family is unknown.
Protein kinase C (PKC) theta is classified as a novel PKC (nPKC). PKC theta is involved in T-cell activation and survival [
,
,
].The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [
,
,
].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [
,
]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [,
,
]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.
Protein kinase C, epsilon is a novel type of protein kinase C (nPKC). PKC epsilon plays essential roles in the regulation of multiple cellular processes linked to cytoskeletal proteins, such as cell adhesion [
], motility, migration [] and cell cycle, functions in neuron growth [,
,
] and ion channel regulation [,
], and is involved in immune response [], cancer cell invasion and regulation of apoptosis [,
].The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [
,
,
].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [
,
]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [,
,
]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.
Protein kinase C, eta type is a member of the novel protein kinase C (nPKC) family. It is involved in the regulation of cell differentiation in keratinocytes [
] and pre-B cell receptor []. PKC eta also mediates regulation of epithelial tight junction integrity [] and foam cell formation []. In addition, it is required for glioblastoma proliferation [] and apoptosis prevention in MCF-7 cells[].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [
,
]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [,
,
]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [
,
,
].
Protein kinase C, delta type is a member of the novel protein kinase C (nPKC) family. PKC delta plays contrasting roles in cell death and cell survival by functioning as a pro-apoptotic protein during DNA damage-induced apoptosis [
], but acting as an anti-apoptotic protein during cytokine receptor-initiated cell death []. PKC delta is also involves in tumor suppression [], required for oxygen radical production by NADPH oxidase [,
] and acts as positive or negative regulator in platelet functional responses [,
].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [
,
]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [,
,
]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [
,
,
].
This coiled-coil domain-containing protein 134 (CCDC134) is a secretory protein that regulates the mitogen activated protein kinase (MAPK) pathway [
]. Overexpression of CCDC134 inhibits transcriptional activity of Elk1 and phosphorylation of Erk and JNK/SAPK but not p38 MAPK []. In humans, CCDC134 interacts with a transcription adaptor hADA2a [].
This protein family occurs in the seadornavirus virus group. Family members have an N-terminal domain for binding double-stranded RNA and are designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus [
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome [
], 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.
This group represents the G0/G1 switch protein 2 (G0S2) [
]. In humans, it promotes apoptosis by binding to BCL2, hence preventing the formation of protective BCL2-BAX heterodimers [].
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.
Sld7 interacts with Sld3 and is required for the proper function of Sld3 at the initiation of DNA replication [
]. The origin association of Sld3, Sld7, and Cdc45 is the key to determining the temporal order of origin firing []. Sld7 is also required for mitochondrial morphology [].
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.
The intermembrane space protein MIX23 regulates or stabilises the mitochondrial protein import machinery and is specifically up-regulated under stress conditions. It is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised. MIX23, also known as Caffeine-induced death protein 2 (Cid2), is evolutionarily conserved and a homologue of the human protein CCDC58 [
].
This entry represents a family of archaeal proteins, including Ta0095 from Thermoplasma acidophilum (
). This protein shows an α/β two-layer sandwich architecture formed by three α-helices and five β-strands. It is thought to bind a negatively charged molecule such as DNA, but its specific function remains unknown [
].
Rad59 is a paralogue of Rad52 and is involved in double-strand breaks (DSBs) DNA repair during vegetative growth via recombination and single-strand annealing [
]. It is required for loading of Rad52 to DSBs [].
This entry includes inner membrane protein RclC which is a reactive chlorine-specific transcription factor in
Escherichia coli. Oxidation of cysteine residues leads to activation of genes required for the response to reactive chlorine species [
].
This family of uncharacterised proteins appears to be restricted to proteobacteria. It includes inner membrane protein RclC (YkgD) from
Escherichia coli, which is a reactive chlorine-specific transcription factor [
].
