Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. Gloeobacter violaceus (strain PCC 7421) (taxid: 251221)
Score = 98.2 bits (243), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 48/82 (58%), Positives = 59/82 (71%)
Query: 7 TGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEH 66
TG G+ YRVLL+D RH+E VAK L + VP++T + ARK F ESR G ++V+V VKEH
Sbjct: 36 TGGGERYRVLLLDHERHTETYVAKALTKAVPNITAEQARKCFFESRLIGKSVVMVAVKEH 95
Query: 67 AEFYAQMMVRGGLRSTIEPDSS 88
AE +A M R GLRSTIEPD S
Sbjct: 96 AEMHAFSMARYGLRSTIEPDGS 117
Source: Physcomitrella patens subsp. patens
Species: Physcomitrella patens
Genus: Physcomitrella
Family: Funariaceae
Order: Funariales
Class: Bryopsida
Phylum: Streptophyta
Superkingdom: Eukaryota
>gi|302829927|ref|XP_002946530.1| hypothetical protein VOLCADRAFT_115933 [Volvox carteri f. nagariensis] gi|300268276|gb|EFJ52457.1| hypothetical protein VOLCADRAFT_115933 [Volvox carteri f. nagariensis]
Score = 59.4 bits (145), Expect = 2e-13
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 11 DSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFY 70
Y+V+L++D + + V +VL +V ++ + A ++ E + G A+V V +E AE
Sbjct: 5 PMYKVILLNDDYTTMEFVVEVLQKVF-GMSEEQATQIMLEVHKEGRAVVGVGTREIAETK 63
Query: 71 AQMMVRGG--LRSTI 83
+ G LR+TI
Sbjct: 64 VAQVHAYGRPLRATI 78
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. Length = 78
>gnl|CDD|178809 PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP
Probab=99.96 E-value=2.8e-29 Score=158.94 Aligned_cols=76 Identities=38% Similarity=0.521 Sum_probs=65.4
Q ss_pred CCCCCceEEEEEcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhhCCcEEEEeeeHHHHHHHHHHHhhcC------Ce
Q 034596 7 TGSGDSYRVLLIDDTRHSEKLVAKVLPQVVPSVTPDDARKLFHESREHGMAIVIVTVKEHAEFYAQMMVRGG------LR 80 (90)
Q Consensus 7 ~~~~~~y~ViL~NDd~~t~e~Vi~~L~~v~p~~s~~~A~~i~~~vH~~G~a~v~~~~~e~AE~~~~~l~~~g------L~ 80 (90)
|+.+++|+|||||||+|||+||+++|+++| |+|.++|.++|++||++|+|+|+.+++++||.++.+|+++| |+
T Consensus 1 ~~~~~~~~vvL~NDe~ht~~~Vi~~L~~~~-~~s~~~A~~~a~~v~~~G~avv~~~~~e~ae~~~~~l~~~g~~~~~PL~ 79 (82)
T PF02617_consen 1 TKEPDMYRVVLWNDEVHTFEQVIDVLRRVF-GCSEEQARQIAMEVHREGRAVVGTGSREEAEEYAEKLQRAGRDSGHPLR 79 (82)
T ss_dssp -BS--EEEEEEE--SSSBHHHHHHHHHHHC----HHHHHHHHHHHHHHSEEEEEEEEHHHHHHHHHHHHHHHHHTT---E
T ss_pred CCCCCceEEEEEcCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHhHcCCEeeeeCCHHHHHHHHHHHHHHhhccCCCeE
Confidence 467899999999999999999999999999 99999999999999999999999999999999999999888 99
Q ss_pred eEE
Q 034596 81 STI 83 (90)
Q Consensus 81 ~~i 83 (90)
++|
T Consensus 80 ~ti 82 (82)
T PF02617_consen 80 ATI 82 (82)
T ss_dssp EEE
T ss_pred EeC
Confidence 987
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 alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-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 beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 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 C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. 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.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
>PF10056 DUF2293: Uncharacterized conserved protein (DUF2293); InterPro: IPR018744 Proteins in this entry are found the bacteria and fungi, they have no known function
