Members of this family are components of the mitotic spindle. Ndc80 acts as a component of the NMS (Ndc80-MIND-Spc7) super complex which has a role in kinetochore function during late meiotic prophase and throughout the mitotic cell cycle. It has been shown that Ndc80 from yeast is part of a complex called the Ndc80p complex [
]. The four Ndc80 complex subunits associate as two rod-like heterodimers (Ndc80:Nuf2 and Spc24:Spc25) []. This complex is thought to bind to the microtubules of the spindle.
This entry represents a group of transmembrane proteins, including mammalian lung seven transmembrane receptor GPR107 and GPR108. GPR107 localizes to the trans-Golgi network and is essential for retrograde transport [
]. This entry also includes proteins from fungi and plants []. The plant proteins in this entry, including CAND6 and CAND7, are predicted to be G-protein coupled receptors [].
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 [,
].On the basis of sequence similarities the following prokaryotic and eukaryotic ribosomal proteins can be grouped:
Bacterial 50S ribosomal protein L10;Archaebacterial acidic ribosomal protein P0 homologue (L10E);Eukaryotic 60S ribosomal protein P0 (L10E).This entry represents the ribosomal protein L10P family, with includes the above mentioned ribosomal proteins.
Ribosomal protein L13 is one of the proteins from the large ribosomal subunit [
]. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.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 consists mainly of uncharacterized proteins from plants. The unc-13 homologue from
Arabidopsis thalianahas been shown to control tethering of the proton ATPase AHA1 to the plasma membrane, and to be essential for the opening of stomata in repsonse to low levels of carbon dioxide and light. The unc13-like protein contains two Munc13 homology domains, which are known to mediate synaptic priming in neuronal exocytosis in animals, and may act similarly for plant stomata [
].
This entry represents a group of cys-rich proteins, including cornifelin and PLAC8 from animals, MCA (MID1-COMPLEMENTING ACTIVITY) and PCR (PLANT CADMIUM RESISTANCE) from Arabidopsis and cell number regulators from maize [
,
].Cornifelin is part of the insoluble cornified cell envelope (CE) of stratified squamous epithelia [
,
]. PLAC8 is required for white adipocyte differentiation in vitro and cell number control in vivo [].Plant transports in this entry include MCA1, MCA2 and PCR1-12. MCA1 and MCA2 mediate Ca2+ uptake [
,
,
], while PCR2 is a zinc exporter involved in both zinc extrusion and long-distance zinc transport [].
This entry represents ethylene-insensitive protein 2. This protein plays a central role in signalling pathways regulated by ethylene (ET), and involved in various processes including development, plant defence, senescence, nucleotide sugar flux, and tropisms [
,
,
,
].
This family includes protein RDM1 from Arabidopsis, which is a a small protein that binds single-stranded methyl DNA, and associates and co-localises with RNA polymerase II, AGO4 and DRM2 in the nucleus. RDM1 is a component of the RNA-directed DNA methylation effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation [
].
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, L27 is found in fungi, plants, algae and vertebrates
[,
].The family has a specific signature at the C 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 [
,
].Ribosomal protein L38e forms part of the 60S ribosomal subunit [
]. This family is found in eukaryotes.
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 consists of mammalian [
], Trypanosoma brucei and fungal L44, Caenorhabditis elegans rpl-36.A, and Haloarcula marismortui LA [].
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 theribosome 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 L28e forms part of the 60S ribosomal subunit [
]. This family is found in eukaryotes. In rat there are 9 or 10 copies of the L28 gene. The L28 protein contains a possible internal duplication of 9 residues [].
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity []:Serine/threonine-protein kinasesTyrosine-protein kinasesDual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins)Protein kinase function is evolutionarily conserved from Escherichia coli to human [
]. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [
], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases [].This domain is found in a large variety of protein kinases with different functions and dependencies. Protein kinase C, for example, is a calcium-activated, phospholipid-dependent serine- and threonine-specific enzyme. It is activated by diacylglycerol which, in turn, phosphorylates a range of cellular proteins. This domain is most often found associated with
.
The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. This entry represents a conserved domain found at the C terminus of Transcription initiation factor TFIID subunit 11 from humans (also known as Transcription initiation factor TFIID 28 kDa subunit, TAFII28 [
]). TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone []. It also interacts directly with TFIIA, acting as a bridging factor that stabilises the TFIIA-TBP-DNA complex []. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four α-helices and three loops arranged as in histone H3 [,
].
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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups:
Eubacterial S16.Algal and plant chloroplast S16.Cyanelle S16.Neurospora crassa mitochondrial S24 (cyt-21).S16 proteins have about 100 amino-acid residues. There are two paralogues in Arabidopsis thaliana, RPS16-1 (chloroplastic) and RPS16-2 (targeted to the chloroplast and the mitochondrion) [].
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 30S ribosomal proteins S7 (bacterial, archaeal, plastid, mitochondrial), and eukaryotic 40S ribosomal proteins S5 (cytoplasmic). 30S ribosomal protein S7 contacts ribosomal proteins S9 and S11. It is also one of the primary rRNA binding proteins - it binds directly to 16S rRNA - where it nucleates assembly of the head domain of the 30S subunit [
]. S7 is located at the subunit interface close to the decoding centre, where it has been shown to contact mRNA. It has also been shown to contact tRNA in both the P and E sites; it probably blocks exit of the E site tRNA.
Actin-binding Rho-activating protein is also known as striated muscle activator of Rho-dependent signaling (STARS) in mouse and myocyte stress 1 (MS1) in rat. STARS acts as an activator of serum response factor (SRF)-dependent transcription, possibly by inducing nuclear translocation of MKL1 or MKL2 and through a mechanism requiring Rho-actin signaling [
,
].
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 ribosomal proteins can be grouped on the basis of
sequence similarities. These proteins have 82 to 87 amino acids. The amino termini are all N alpha-acetylated. The N-terminal halves of the protein molecules are highly conserved in contrast to the carboxy-terminal parts [
].
Meiosis-specific protein MEI4 is required for meiotic induction of recombination, viable spore production and chromosome synapsis. It is a component of the MER2-MEI4-REC114 complex which seems to be required for meiotic double-strand break (DSB) formation [
,
]. In Schizosaccharomyces pombe it is known as Rec24 [,
].
Growth hormone receptor binding protein is produced either by proteolysis of the growth hormone receptor (GHR) at the cell surface thereby releasing its extracellular domain, the GHBP (growth hormone-binding protein), or, in rodents, by alternative processing of the GHR transcript. The sheddase proteolytic enzyme responsible for the cleavage is TACE (tumour necrosis factor-alpha-converting enzyme) [
,
].Growth hormone (GH) binding to GH receptor is the initial step that leads to the physiological functions of the hormone []. The biological effects of GHBP are determined by the serum levels of GH, which can vary. Low levels of GH can result in a dwarf phenotype and have been positively correlated with an increased life expectancy. High levels of GH can lead to gigantism or a clinical syndrome termed acromegaly and have been implicated in diabetic eye and kidney damage [].
These conserved proteins from Gram-positive bacteria possess most of the motifs characteristic of a variety of
enzymatically active phosphoesterases [], including acid and alkaline phosphatases,phosphoprotein phosphatases, 5'-nucleotidase, bis(5'-nucleosyl)-tetraphosphatase (symmetrical), sphingomyelin
phosphodiesterase, 2',3'-cylic-nucleotide 2'-phosphodiesterase, and 3',5'-nucleotide phosphodiesterase CpdA.Interestingly, the catalytically active histidine usually found has been replaced by asparagine in these
proteins, so their catalytic activity is speculative.
This entry includes RBBP5 from animals, RBL from plants and Swd1 from yeasts. Swd1 is a component of the SET1C/COMPASS complex, a complex that methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres [
,
].Retinoblastoma-binding protein 5 (RBBP5) is important for development in embryonic stem cells, regulating gene induction and H3 'Lys-4' methylation at key developmental loci [
]. It is a component of the SET1 histone methyltransferase complex [], and methyltransferase-containing (COMPASS) complexes MLL1, MLL2/3 and MLL4 [,
].Arabidopsis RBL is also a component of a COMPASS-like complex that mediates histone H3 lysine-4 trimethylation to control floral transition and plant development [
].
Activity-regulated cytoskeleton-associated protein
Type:
Family
Description:
The Activity-Regulated Cytoskeleton-associated protein (Arc), also referred to as Arg3.1 (Activity-Regulated Gene), is an immediate-early gene predominantly found in mammals that has been related to synaptic plasticity, learning and memory processes [
,
,
,
,
]. It has been shown that Arc/Arg3.1 expression increases with strong synaptic activation []. Its mRNA is transported to activated dendritic regions, conferring on the protein-distribution temporal correlation with the inducing stimulus and spatial specificity [,
].Via interactions with dynamin and endophilin isoforms, the Arc/Arg3.1 protein enhances receptor endocytosis [
]. Specifically, it modulates trafficking of neuronal AMPA-type glutamate receptors (AMPARs) by accelerating endocytosis and reducing surface expression []. In particular, Arc/Arg3.1 has been shown to reduce the number of GluR2/3 receptors, leading to a decrease in AMPAR-mediated synaptic currents []. These observations are consistent with a role in homeostatic regulation of synaptic strength [,
].
The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO [
,
,
]. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency [,
]. MEX-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms [,
,
]. It has been shown that these proteins are deregulated in several cancers and affects apoptosis regulation, antigen processing, and presentation, which, therefore, contribute to the immune evasion of tumour cells [,
].They are characterised by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger [
]. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway [].
Aurora-A, a protein kinase required for centrosome maturation, spindle assembly and asymmetric protein localisation during mitosis, is activated by Aurora borealis protein at the onset of the mitotic cycle []. Bora is a nuclear protein in interphase cells, but is excluded from the nucleus and translocates to the cytoplasm in a Cdc2-dependent manner when the cell enters mitosis []. It has been suggested that activation of Cdc2 initiates the release of Bora into the cytoplasm, where it binds and activates Aurora-A [].
Formyl Peptide Receptor-Like 1 (FPRL1)-inhibitory protein (also termed FLIPr) has been shown to inhibit calcium mobilisation in neutrophils [
]. There is evidence that FLIPr binds to FPRL1 and, at higher concentrations, to FPR [], impairing the leukocyte response to FPRL1 agonists. It has revealed unknown inflammatory ligands during S.aureus infection and, as an FPRL1 antagonist, may facilitate development of therapeutic agents in FPRL1-mediated inflammatory diseases [].
Vac17 serves as an adaptor protein recruiting vacuole vesicles to the actin cable tracks by its dual interaction with Vac8 and the Myo2 motor protein [
]. It is directly phosphorylated by Cdk1. Vac17 plays an important role in vacuole inheritance and segregation in cell division [].
This entry includes TP53-binding protein 1 (TP53BP1, also known as p53BP1 or 53BP1) and its orthologues, such as DNA repair protein RAD9 from S.cerevisiae and Crb2 from S.pombe [
,
,
,
,
,
,
,
,
]. TP53BP1 is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis [,
]. TP53BP1 and its homologue from C.elegans hsr-9 contain two tandem BRCT domains, while the fungal orthologues contain one BRCT domain [,
]. Crb2, is a checkpoint mediator required for the cellular response to DNA damage [].
This entry represents PutA, which is a bifunctional enzyme with proline dehydrogenase (PDH) and delta 1-pyrroline-5-carboxylate dehydrogenase (P5CDH) activities [
]. PutA also acts as a transcriptional repressor of proline utilisation (put) genes [].
Aflatoxins belong to a family of decaketides that are produced as secondary metabolites by Aspergillus flavus and Aspergillus parasiticus [
]. The aflatoxin biosynthetic pathway involves several enzymatic steps that appear to be regulated by the aflR genes in A. flavus and A. parasiticus. AflR encodes a protein that contains a cysteine-rich motif. Several fungal transcriptional activator proteins contain this motif, which binds DNA in a zinc-dependent fashion (occurs in fungal transcriptional regulatory proteins) [,
].This domain is found in the aflatoxin regulatory protein (AflR) and related fungal sequences. AflR is involved in the regulation of the biosynthesis of aflatoxin in the fungal genus Aspergillus [
]. It occurs together with the fungal Zn(2)-Cys(6) binuclear cluster domain ().
This entry also includes Sterigmatocystin biosynthesis regulatory protein [
]. Sterigmatocystin is related to aflatoxin.
Ligands of the Delta/Serrate/lag-2 (DSL) family and their receptors, members of
the lin-12/Notch family, mediate cell-cell interactions that specify cell fate in invertebrates and vertebrates. In Caenorhabditis elegans, two DSL genes, lag-2 and apx-1,influence different cell fate decisions during development [
]. Molecular interaction between Notch and Serrate, another EGF-homologous transmembrane protein containing a region of striking similarity to Delta, has been shown and the same two EGF repeats of Notch may also constitute a Serrate binding domain [,
].
The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body [
]. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament [
]. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively.The sequences of the FlgH, FlgI and FliF gene products have been determined [
]. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences [,
]. FlgH is predicted to have an extensive β-sheet structure, in keeping with other outer membrane proteins, and FlgI is thought to have even more β-structure content []. Several aspects of the DNA sequence of these genes and their surrounds suggest complex regulation of the flagellar gene system.
Members of this family are linker polypeptides that are associated with
phycobilisomes. Phycobiliproteins (biliproteins) are accessory pigments thatserve as receptors of light energy for photosystem II. Phycobilisomes are
highly organised complex structures of biliproteins and linker polypeptides.The linker polypeptides are involved in the attachment of phycobilisomes to
the thylakoid membrane and in the assembly of biliproteins intophycobilisomes.The three dimensional structure of an
electrophoretically purified allophycocyanin-linker complex has beendetermined [
]. The asymmetric unit contains twoside-to-side associated trimeric (alphabeta)
3allophycocyanin
complexes comprising the linker polypeptide in a defined orientation insidethe trimer. The linker representing a protein fold related to the prosegment
of procarboxypeptidase A is in contact with only two of the threebeta-subunits and directly interacts with the corresponding chromophores of
these proteins.For additional information please see [
,
].
The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in
vivo, and may play a role in maintaining the structural and functionalstability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner [
]. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].
This entry represents a group of plant meiosis-specific proteins, such as AtASY3 from Arabidopsis and PAIR3 from rice. They are coiled-coil domain proteins required for normal meiosis [
]. PAIR3 is an axial element and part of the synaptonemal complex (SC) that forms between homologous chromosomes during meiosis []. Members of this family are homologues of SYCP2 from vertebrates and fungal Red1/Red10 [].
Viral protein 3 (VP3) specifically binds to GTP and contains mRNA guanylyltransferase and mRNA (guanine-N(7)-)-methyltransferase activities. It is a multifunctional enzyme involved in mRNA capping. It catalyses the formation of the 5' cap structure on the viral plus-strand transcripts [
,
]. Structure analyses revealed that it contains a variable N-terminal domain, a central guanine-N7-methyltransferase domain with an additional inserted domain, and a C-terminal guanylyltransferase and RNA 5'-triphosphatase domain. The insertion in the guanine-N7-methyltransferase domain is a ribose-2'-O-methyltransferase domain for most rotavirus species [].
This is a family of unknown function found in Cytomegalovirus. One of the family members US30 is a putative membrane glycoprotein with one predicted trans-membrane region.
Members of this family include UL42 proteins found in Human cytomegalovirus (HCMV). UL42 has two Pro-Pro-X-Tyr (PPxY) sequences, a hydrophobic region at the C terminus and no N-terminal signal peptide. These features are shared with herpes simplex virus (HSV) UL56. UL42 has a putative C-terminal trans-membrane region. HCMV UL42 interacts with Itch, a member of the Nedd4 family of ubiquitin E3 ligases, through its PY motifs as observed in HSV UL56, suggestive of a regulatory function [
].
This is a family of unknown function found in SARS and SARS-like coronaviruses. It includes uncharacterised protein 14 from SARS coronavirus 2 (SARS-CoV-2), Human SARS coronavirus (SARS-CoV) and Bat coronavirus Rp3/2004 (SARS-like coronavirus Rp3) []. In SARS-CoV, Orf14 is completely contained within the ORF encoding the nucleocapsid protein (N) []. In SARS-CoV-2 uncharacterised protein 14 is predicted to contain one transmembrane helix.
Family members such as protein p6 from Bacillus subtilis phage phi29 bind double-stranded DNA, forming a large nucleoprotein complex all along the viral genome, and have been proposed to be an architectural protein with a global role in genome organization. P6 is also involved in viral transcriptional control, repressing the C2 early promoter located at the right DNA end, and together with the viral regulatory protein p4, repressing early promoters A2b/A2c and activating late promoter A3 [
].
Sulphur globules are membrane-bounded intracellular globules, used by purple sulphur bacteria to transiently store sulphur during the oxidisation of reduced sulphur compounds [
]. This proteobacterial family contains structural proteins of these sulphur globules, and includes sulphur globule protein CV1 (SgpA) and sulphur globule protein CV2 (SgpB).
This entry represents Ubiquitin-like protein 4A from humans (UBL4A) and similar proteins found in animals and fungi. UBL4A is part of a ubiquitin ligase-associated multiprotein complex that chaperones retrotranslocated polypeptides on its way to the proteasome to improve the efficiency of the endoplasmic reticulum-associated degradation (ERAD) [
]. The complex also functions as a sorting platform for proteins of the secretory pathway that are mislocalized to the cytosol either delivering them to the proteasome for degradation or to the endoplasmic reticulum []. The homologue in Saccharomyces cerevisiae, Ubiquitin-like protein MDY2, is required for efficient mating [].
This entry includes a group of kinesin-like proteins, including human Eg5/KIF11, its orthologue from Drosophila Klp61F, BimC from Emericella nidulans and CIN8 from Saccharomyces cerevisiae. These are spindle pole proteins, which participate in spindle assembly and chromosome segregation during cell division, required for spindle body separation [
,
].
This entry includes DCC-interacting protein 13-alpha/beta from humans (DIP13A/B, also known as APPL1/2) and similar proteins predominantly found in vertebrates. DIP13A/B are multifunctional adapter proteins that bind to various membrane receptors, nuclear factors and signalling proteins to regulate many processes, such as cell proliferation, immune response, endosomal trafficking and cell metabolism [
,
,
,
,
]. DIP13B may also affect adult neurogenesis in hippocampus and olfactory system via regulating the sensitivity of glucocorticoid receptor [,
]. These proteins consist of a BAR and a PH domain near the N-terminal, and the two domains are thought to function as a unit (BAR-PH domain) [
]. At the C-terminal, they have a PTB domain []. Lipid binding assays show that the BAR, PH, and PTB domains can bind phospholipids [].
This entry represents the JNK (c-Jun N-terminal kinase)-interacting proteins (JIP) scaffold family, a group of scaffold proteins that regulate signalling by stress-activated MAPKs (mitogen-activated protein kinase) [
], including C-Jun-amino-terminal kinase-interacting protein 1/2 from humans (JIP1/2). These proteins selectively mediate JNK signalling by aggregating specific components of the MAPK cascade to form a functional JNK signalling module and are required for JNK activation in response to excitotoxic stress []. They regulate the activation of MAPK8/JNK1 and differentiation of CD8+ T-cells []. JIP-1 from Drosophila melanogaster, also known as JNK-interacting protein 1, is known to play roles in fast axonal transport that are important for neuron structure and function []. Members of this family are found in animals.
This entry includes nitrile-specifier protein 1/2/3 from Arabidopsis. Nitrile-specifier protein convert allylglucosinolate and benzylglucosinolate to their corresponding simple nitriles in the presence of myrosinase. They contain lectin-like jacalin domains, which share a common ancestry with the jacalin domains of the putative Arabidopsis myrosinase-binding proteins MBP1 and MBP2 [
].
A Saccharomyces cerevisiae (Baker's yeast) member of this family (PGA2,
) is a single pass membrane protein which is implicated in protein trafficking and processing of glycosylated proteins [
,
].
Acid shock protein is required for growth and/or survival in acidic conditions. It is needed for the adaptation process at pH 4.5 that enables cells to survive at extremely low pH (pH 2.0) [
].
This family of proteins is regulated in B. subtilis by SigD [
], and is likely to be involved in motility or flagellin production. Proteins in this family are approximately 60 amino acids in length, and contain two highly conserved asparagine residues.
Microspherule protein 1 (MCRS1 or MSP58) is an RNA-binding protein that interacts with Daxx transcriptional regulator, relieving its repressor activity. Overexpression of MCRS1 leads to translocation of Daxx to the enlarged nucleoli in COS-1 or 293 cells [
]. It also interacts with fragile X messenger ribonucleoprotein 1 (FMRP), which represses specific mRNAs being transported as silent ribonucleoparticles from the cell body of a neuron to the distant synapse. MCRS1 binds to the G-quadruplex structures of the mRNA []. MCRS1 is a component of the NSL complex [], the MLL1/MLL complex [], and is a putative regulatory component in the chromatin remodeling INO80 complex []. The isoform MCRS2 is a cell-cycle-dependent protein which accumulates in the early S phase, and interacts with the telomerase-inhibitory protein LPTS/PinX1 [].
Caulimoviruses are encapsidated plant viruses that contain circular double-stranded DNA [
]. Members of the group include Cauliflower mosaic virus [], Carnation etched ring virus (CERV) [], Figwort mosaic virus [] and Soybean chlorotic mottle virus []. The viral coat proteins are quite similar, containing a fairly hydrophilic N-terminal region and a highly-basic C-terminal domain, which may be involved in DNA-binding. The sequences contain the motif CxxCxxxHxxxC, which is similarly found in the nucleic acid binding protein of retroviruses [].
This entry represents a group of fungal mitochondria proteins, known as Pet127, that stimulate mitochondrial RNA degradation [
,
]. Pet127 has been classified as part of the PD-(D/E)XK nuclease superfamily including a full set of active site residues [].
This family includes the B. subtilis YdjO protein (
), which is functionally uncharacterised. Note - this is not a homologue of E. coli YdjO (). B. subtilis YdjO is cold-inducible [
]. Its expression is induced by the extracytoplasmic function sigma factor sigma-W [].
The nucleotide sequence of the RNA of Potato leafroll virus (PLrV) has been determined [
,
]. The sequence contains six large ORFs. The 3' coding region encodes three polypeptides: a 23K coat protein, a 17K polypeptide encoded in a different frame, and a 53K polypeptide, immediately following the coat protein sequence in the same frame. It has been suggested that the 53K polypeptide is translated by readthrough of the amber termination codon of the coat protein gene. The amino acid sequences encoded within the 3' region show many similarities to analogous polypeptides of Barley yellow dwarf virus (BYDV), and Beet western yellows virus (BWYV). It is possible that the ORF5 protein is a VPG-precursor from which, at the onset of RNA synthesis, the VPG molecule is released, in a similar fashion to that proposed for Cowpea mosaic virus (CPMV).
This region of the Zds1 protein is critical for sporulation and has also been shown to suppress the calcium sensitivity of Zds1 deletions [
]. The C-terminal motif is common to both Zds1 and Zds2 proteins, both of which are putative interactors of Cdc55 and are required for the completion of mitotic exit and cytokinesis. They both contribute to timely Cdc14 activation during mitotic exit and are required downstream of separase to facilitate nucleolar Cdc14 release[].
RPS12 is a ribosomal protein encoded by the kinetoplast mitochondrion of Kinetoplastida protists such as Trypanosoma. Homologous RPS12 proteins in bacterial ribosomes participate in stabilizing the second base pair of the codon-anticodon duplex in the A site and is likely to be critical for the fidelity of decoding process. A similar role can be anticipated for this protein in mitochondrial ribosomes. This has been shown where the product of edited RPS12 mRNA translation represented a component of the mitoribosome's small subunit [
].
This is a family of metal-binding proteins which are involved in resistance to heavy-metal ions [
,
]. These proteins form a four-helix hooked hairpin, consisting of two long alpha helices each flanked by a shorter alpha helix. They bind a metal ion in a type-2 like centre [] and contain two copies of an LTXXQ motif.
It has been shown [
] that integral membrane proteins that mediate the uptakeof a wide variety of molecules with the concomitant uptake of sodium ions
(sodium symporters) can be grouped, on the basis of sequence and functionalsimilarities into a number of distinct families. One of these families [
] isknown as the sodium:dicarboxylate symporter family (SDF).
Such re-uptake of neurotransmitters from the synapses, is thought to be an important mechanism for terminating their action, by removing these chemicals from the synaptic cleft, and transporting them into presynaptic nerve terminals, and surrounding neuroglia. this removal is also believed to prevent them accumulating to the point of reaching neurotoxic [
,
].The structure of these transporter proteins has been variously reported to
contain from 8 to 10 transmembrane (TM) regions, although 10 now seems tobe the accepted value.This entry represents cell membrane proteins which are responsible for the transport of dicarboxylates such assuccinate, fumarate, and malate from the periplasm across the membrane [
]. They belong to the sodium:dicarboxylate (SDF) symporter(TC 2.A.23) family.
This domain is found in Vaccinia and Variola viruses. Family members include E7R gene product. Vaccinia virus (VV) is a large double-stranded DNA virus that replicates in the cytoplasm of infected cells. Many viruses express proteins that are modified by myristic acid. Myristic acid is a 14-carbon fatty acid that is cotranslationally transferred to the penultimate glycine residue found within the consensus sequence MGXXX(S/T/A/C/N) (where X is any amino acid) at the amino terminus of target proteins. E7R proteins in Vaccina virus have been shown to be myristylated. The expressed E7R protein has also been found to reside within mature infectious virions [
].
Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies [
]. HHV6 A/B encode two putative chemokine receptors and a chemokine-like protein. The HHV6 U83 gene encodes a CC chemokine, which functions as a highly selective and efficacious agonist for the human CCR2 receptor, both in respect of signal transduction and the ability to induce chemotaxis. Homologues of the U83 gene products are found in Human cytomegalovirus encoded chemokines vCXC1 and vCXC2.HHV-6 U83, also known as vCCL4, contains a region with the CC/CX3C chemokine motif and a glycosaminoglycan (GAG)-binding epitope, BBXB (B being a basic residue), found right before the third Cys residue, which very likely forms a disulfide bridge back to the first Cys of the protein [
]. This gene is the only HHV-6A/B divergent gene that is specific for these viruses. The U83 chemokine gene is distinct between HHV-6A and HHV-6B strains, encoding up to 13 amino acid differences. The HHV-6A (U83A) and HHV-6B (U83B) chemokines have distinct specificities which determine chemoattraction or diversion of different leukocyte subsets for infection or immune evasion, thus an early component of cellular tropism as well as mediator of innate immunity. U83 also has a varied gene structure, with N-terminal length variation determining production of the encoded mature secreted chemokine, coupled with control by cell-directed splicing which truncates the chemokine gene early in replication to encode an antagonist. The 'long' active form of U83A has a unique broad specificity for receptors CCR1, CCR4, CCR5, CCR6 and CCR8 present on plasmacytoid and myeloid dendritic and monocyte/macrophage antigen presenting cells, as well as both TH1 and TH2 skin homing lymphocytes and NK cells; it is also amongst the highest affinity ligands for CCR5 and inhibits HIV-1 binding at this coreceptor. U83A can both block and divert human chemokine action while occupying the human chemokine receptors [].
This entry represents a group of insect proteins that play a role in the establishment of the polarity of the oocyte. Proteins in this entry include exuperantia (Exu), which is a an RNA-binding pseudonuclease associated with bicoid mRNA and required for its localization. It interacts with its target RNA as a homodimer [
].
This is a family of unknown function found in Phytoreovirus. Family members include the Rice dwarf virus Pns11 and Pns12 proteins. Rice dwarf virus (RDV) is an icosahedral, double-layered particle. The viral genome consists of 12 segmented dsRNAs that encode seven structural (P1, P2, P3, P5, P7, P8 and P9) and five non-structural (Pns4, Pns6, Pns10, Pns11 and Pns12) proteins. Pns11 is known to bind nucleic acids and Pns12 is a phosphorylated protein. The non-structural proteins Pns6, Pns11 and Pns12 of RDV are the major constituents of the matrix of viral inclusions in which the assembly of progeny virions and the synthesis of viral RNA are thought to occur [
].
This entry represents the upper collar protein (also known as portal protein Gp10) from various bacteriophage. The upper collar protein of Bacteriophage phi-29 is composed of twelve 36kDa subunits with 12-fold symmetry. It consists of two domains: an α-helical bundle domain and a β-barrel domain. This protein is located between the head and the tail of the bacteriophage and acts as the central component of a rotary motor that packages the genomic dsDNA into pre-formed proheads. This motor consists of the upper collar protein, surrounded by a 29-encoded, 174-base, RNA and a viral ATPase protein [
,
].
The bacterial protein RecR is an important regulator in the RecFOR homologous recombination pathway during DNA repair [
,
,
,
]. It acts with RecF and RecO forming a complex that facilitates the loading of RecA onto ssDNA [,
]. RecR is a zinc metalloprotein consisting of a N-terminal helix-hairpin-helix (HhH) motif, a middle region containing a zinc finger motif and a Toprim domain, and a C-terminal domain comprising a divergent Walker B motif and a C-terminal helix [,
]. This entry represents RecR's main structural domain, which consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif [
].
This entry represents proteins found in nematodes. They complex with MSP (major sperm protein) to allow motility [
]. Their action is quite similar to the action of bacterial actin molecules.
This entry represents the class I phage major coat protein Gp8 or B. The coat protein is largely α-helix with a slight curve [
]. It is inserted in the host inner membrane, where filamentous phages are assembled and then extruded across the cellular envelope, without killing the bacterial host [].The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about
7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of thesignal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure
that encapsulates the viral DNA [].
Casparian strip membrane proteins (CASPs) are four-membrane-span proteins that mediate the deposition of Casparian strips in the endodermis by recruiting the lignin polymerization machinery. CASP-like proteins (CASPLs) contain a CASP domain and are also able to form transmembrane scaffolds. The transmembrane domains, particularly the first (TM1) and the third (TM3) are highly conserved among these proteins. CASPLs can be classified in five groups (1-5); this family represents group 5 (CASPL5). In Arabidopsis, CASPLs showed specific expression in a variety of cell types, such as trichomes, abscission zone cells, peripheral root cap cells, and xylem pole pericycle cells [].
RodZ are cytoskeletal proteins that are involved in bacterial cell-shape control through regulation of the length of the long axis [
]. They are transmembrane proteins, with a cytoplasmic N-terminal domain that includes a helix-turn-helix motif, and a large periplasmic C-terminal domain.
This entry includes a group of pre-RNA processing ribonucleoproteins (RNPs), including Nop56/Nop58 from animals and their homologue, Nop5, from archaea. Proteins in this family contains the Nop domain, which is a RNP binding module, exhibiting RNA and protein binding surfaces. It is oval-shaped and exclusively α-helical [
,
]. Nop56 and Nop58 are components of box C/D small nucleolar ribonucleoprotein (snoRNP) particles [,
].
This entry represents a family of minor capsid proteins found in a number of bacteriophages including Bacteriophage A118. The function of these proteins is not known.
This entry represents viral proteins of approximately 100 amino acids in length. p12I binds to the immature beta and gamma-c chains of the interleukin-2 receptor retarding their translocation to the plasma membrane. p12I forms dimers which bind to these chains [
].
Mistic is an integral membrane protein that folds autonomously into the membrane [
]. It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations [].
Spore formation in Bacillus subtilis involves a highly asymmetric cell division where the chromosome destined to enter the spore needs to move to the extreme pole of the cell in order to be captured in the prespore cell. This is accomplished by a specialised that moves the oriC region of the chromosome close to the cell pole before septation. RacA, a DNA-binding protein, is part of this system and is required for proper chromosome separation [
,
]. It binds in a dispersed manner throughout the chromosome but preferentially to sites clustered in the origin portion of the chromosome, causing condensation of the chromosome and its remodelling into an elongated, anchored structure.
The name CRIP, for cyclophilin-RNA interacting protein, has been proposed for this family of proteins that comprise a cyclophilin-type peptidyl-prolyl isomerase domain, an RNA recognition motif, followed by a region rich in glutamate and lysine (EK domain) and a C-terminal string of serines [
]. The family includes among others Paramecium tetraurelia KIN241 [], human cyclophilin-like protein PPIL4 [], Arabidopsis thaliana AtCYP59 [], and Caenorhabditis elegans sig-7 [].
This entry represents a group of bacterial proteins, including TasA from Bacillus subtilis. Microbes construct architecturally complex and ordered communities called biofilms through production of an extracellular matrix composed of an exopolysaccharide and the amyloid-like protein TasA [
]. TasA has the propensity to polymerize into fibres enriched in beta sheets and highly resistant to degradation or denaturation []. TasA fibres are used by B. subtilis to build a network that connects cells and may organize the rest of the components of the extracellular matrix [].
This entry represents a family of Streptococcal proteins that contain a number of repeated His-X-X-His-X-His (histidine triad) motifs. Members of the family are suggested to cleave human complement component 3, and family member PhpA has been shown in vaccine studies to be a protective antigen in mice [
].
Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons [
,
]. This entry separates members from the phosphate ABC transporter phosphate binding proteins described by .
Members of this protein family are found exclusively in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) containing organisms. They are found in operon contexts with RAMP (Repeat-Associated Mystery Protein), which is also linked to CRISPR.
BIN4 (also known as MIDGET) is a plant-specific, DNA binding protein that acts as a component of the plant DNA topoisomerase VI complex. BIN4 is required for endoreduplication [
]. Loss of BIN4 triggers an ATM- and ATR-dependent DNA damage response in postmitotic cells, and this response coincides with the upregulation of the cyclin B1;1 gene, suggesting a functional link between DNA damage response and endocycle control [,
].
