This entry includes ClpS from bacteria and chloroplastic CLPS1/2 from plants. ClpS binds directly to N-terminal destabilising residues through its substrate-binding site distal to the ClpS-ClpA interface, and targets these substrates to the ClpAP protease for degradation [, ].ClpS is a small alpha/beta protein that consists of three α-helices connected to three antiparallel β-strands []. The protein has a globular shape, with a curved layer of three antiparallel α-helices over a twisted antiparallel β-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue β-strand, which is flanked by two other β-strands in a small β-sheet.
In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins [].ClpS is a small alpha/beta protein that consists of three α-helices connected to three antiparallel β-strands []. The protein has a globular shape, with a curved layer of three antiparallel α-helices over a twisted antiparallel β-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue β-strand, which is flanked by two other β-strands in a small β-sheet.
This domain is the conserved central region of bacterial collagen-like proteins (CLPs). Similar to animal collagens, bacterial CLPs contain the G-X-Y repeat motifs []. They are involved in pathogenicity, immune response elicitation and host-parasite interactions, possibly evolving as mimics of host proteins containing G-X-Y motifs [].
UBR box family is a unique class of E3 ligases that recognise N-degrons or structurally related determinants for ubiquitin-dependent proteolysis. They belong to the N-end rule pathway which relates the identity of the N-terminal residue of a protein with its half-life, recognising destabilising ones. Some of the functions of this pathway include the control of peptide import, the fidelity of chromosome segregation, the regulation of apoptosis, as well as regulation of meiosis in yeasts and metazoans, leaf senescence in plants, and cardiovascular development in mammals []. These proteins contain an N-terminal UBR box (a substrate-binding domain), which is highly conserved among UBR family members, a cysteine- and histidine-rich RING (RING-H2) domain, which is present in a larger class of E3 ubiquitin ligases and some additional domains that vary among UBR family members, like these described in UBR1 []: ClpS, a region of sequence similarity to prokaryotic ClpS which acts as an accessory subunit that contributes to recognition of degrons by the ATP-dependent protease ClpAP, a BRR (basic residue-rich region), a conserved motif that contributes to the binding of yeast UBR1 to the E2 enzyme RAD6, and conserved regions [, , ].This entry represents the C-terminal domain which includes a conserved region found in E3 ubiquitin-protein ligase UBR1, 2, 3 from animals, UBR1/11 from fission yeast, and also in PRT6 from Arabidopsis thaliana [].
O-Glycosyl hydrolases () are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrateand a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.The glycosyl hydrolases family 18 (GH18) is widely distributed in all kingdoms and contains hydrolytic enzymes with chitinase or endo-N-acetyl-beta-D-glucosaminidase (ENGase) activity as well as chitinase-like lectins (chi-lectins/proteins (CLPs). Chitinases () are hydrolytic enzymes that cleave the beta-1,4-bond releasing oligomeric, dimeric (chitobiose) or monomeric (N-actetylglucosamine, GlcNAc) products. ENGases () hydrolyze the beta-1,4 linkage in the chitobiose core of N-linked glycans from glycoproteins leaving one GlcNAc residue on the substrate. CLPs do not display chitinase activity but some of them have been reported to have specific functions and carbohydrate binding property []. This family also includes glycoproteins from mammals, such as oviduct-specific glycoproteins.The catalytic domain of GH18s has a common (beta/alpha)8 triosephosphate isomerase (TIM)-barrel structure, which consists of a barrel-like framework made from eight internal parallel β-strands that are alternately connected by eight exterior α-helices. The active site motif DxxDxDxE is essential for the activity of the GH18 catalytic domain. [, , ].
The glycosyl hydrolases family 18 (GH18) [E1]is widely distributed in all kingdoms, including viruses, bacteria, plants, fungi and animals. The GH18 family contains hydrolytic enzymes with chitinase or endo-N-acetyl-beta-D-glucosaminidase (ENGase) activity as well as chitinase like lectins (chi-lectins/proteins (CLPs). Chitinases (EC 3.2.1.14) are hydrolytic enzymes that cleave the beta-1,4-bond releasing oligomeric, dimeric (chitobiose) or monomeric (N-actetylglucosamine, GlcNAc) products. ENGases (EC ) hydrolyse the beta-1,4 linkage in the chitobiose core of N-linked glycans from glycoproteins leaving one GlcNAc residue on the substrate. CLPs do not display chitinase activity but some of them have been reported to have specific functions and carbohydrate binding property. The catalytic domain of GH18s may be connected to one or several substrate binding modules (CBMs), which enhance binding of enzymes to insoluble substrates. Certain GH18s also contain peptide signals for localization such as an N-terminal secretion peptide, a C-terminal glycosyl-phosphatidylinositol (GPI) anchor signal for attachment to the plasma-membrane, or N- or O-linked glycosylation sites for oligosaccharide modifications [, , , , , , , , ].The catalytic domain of GH18s has a common (beta/alpha)8 triosephosphate isomerase (TIM)-barrel structure, which consists of a barrel-like framework made from eight internal parallel β-strands that are alternately connected by eight exterior alpha helices. The active site motifDxxDxDxE is essential for the activity of the GH18 catalytic domain. The Glu (E) in this motif acts as the catalytic proton donor, and the last Asp (D(3))is supposed to contribute to the stabilization of the essential distortion of the substrate [, , , , ].This entry represents the active site of GH18.
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 superfamily represents a domain found at the C terminus of ribosomal proteins L7 and L12, and also in the adaptor protein ClpS, forming an alpha/beta sandwich [].The L7 and L12 ribosomal proteins are part of the large50S ribosomal subunit, and occur in four copies organised as two dimers. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post-translational modification of the addition of an acetyl group to the N terminus of L7 [].ClpS is an adaptor protein that influences protein degradation through its binding to the N-terminal domain of the chaperone ClpA in the ClpAP chaperone-protease pair. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins [].
