>gi|91089255|ref|XP_969352.1| PREDICTED: similar to 60S ribosomal protein L7/L12 [Tribolium castaneum] gi|270011463|gb|EFA07911.1| hypothetical protein TcasGA2_TC005486 [Tribolium castaneum]
Score = 74.9 bits (185), Expect = 5e-19
Identities = 32/89 (35%), Positives = 49/89 (55%), Gaps = 1/89 (1%)
Query: 7 AQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESI 66
A A AA E ++ F V L + +K+ +IKE++ + G+ L +AK VES
Sbjct: 40 AAAAAPAAAAAAAAEAEEKTEFDVVLESFGAAKKIAVIKEVREIT-GLGLKEAKDLVESA 98
Query: 67 PAVVKTDVTKEEAEALKASLAKVGGEVSV 95
P V+K V+KEEAE +K L + G +V +
Sbjct: 99 PKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127
Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises L7/L12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that L7/L12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors. In eukaryotes, the proteins that perform the equivalent function to L7/L12 are called P1 and P2, which do not share sequence similarity with L7/L12. However, a bacterial L7/L12 homolog is found in some eukaryotes, in mitochondria and chloroplasts. In archaea, the protein equivalent to L7/L12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to L7/L12. Length = 127
>gnl|CDD|201294 pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal domain
Score = 47.7 bits (114), Expect = 2e-08
Identities = 35/90 (38%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 7 AQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESI 66
A A AA E EEK + F V L K K+ +IK ++ L G+ L +AK VE
Sbjct: 40 AAAAAGAAAAEAAEEK---TEFDVVLKSAGGK-KIAVIKVVRELT-GLGLKEAKDLVEGA 94
Query: 67 PAVVKTDVTKEEAEALKASLAKVGGEVSVE 96
P V+K V+KEEAE +K L + G +V ++
Sbjct: 95 PKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124
Length = 124
>gnl|CDD|233152 TIGR00855, L12, ribosomal protein L7/L12
Score = 44.7 bits (106), Expect = 2e-07
Identities = 35/94 (37%), Positives = 49/94 (52%), Gaps = 5/94 (5%)
Query: 2 TISIFAQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKK 61
+ A A AAA EE ++ F V L D K+ +IK ++ + G+ L +AK
Sbjct: 34 AAPVAAGAAGAAAAAAAAEE---KTEFDVILKGAGDN-KIAVIKVVREI-TGLGLKEAKD 88
Query: 62 FVESIPAVVKTDVTKEEAEALKASLAKVGGEVSV 95
VE P V+K V+KEEAE LK L + G +V V
Sbjct: 89 LVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEV 122
Ribosomal proteins L7 and L12 are synonymous except for post-translational modification of the N-terminal amino acid. THis model resembles pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 123
>gnl|CDD|214358 CHL00083, rpl12, ribosomal protein L12
Score = 44.6 bits (106), Expect = 4e-07
Identities = 32/89 (35%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 7 AQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESI 66
A A AA EE EEK + F V L + +++ ++K ++ L G+ L +AK+ VES+
Sbjct: 46 APAAAAAQAAEEVEEK---TEFDVILEEVPADKRIAVLKVVRSLT-GLGLKEAKELVESL 101
Query: 67 PAVVKTDVTKEEAEALKASLAKVGGEVSV 95
P +K ++KEEAE K L + G +V +
Sbjct: 102 PKTIKEGISKEEAEEAKKQLEEAGAKVII 130
Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
>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.
>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=87.16 E-value=2.1 Score=27.52 Aligned_cols=69 Identities=23% Similarity=0.300 Sum_probs=49.4
Q ss_pred cceeEEEEeeCCCCCchHHHHHHHHhhcCCCHHHHHHHHhhcC----hhhhhcCCHHHHHHHHHHHHhCC------cEEE
Q psy4492 25 QSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIP----AVVKTDVTKEEAEALKASLAKVG------GEVS 94 (96)
Q Consensus 25 kt~f~V~L~~~~~~kKi~vIK~VR~i~t~LgLkEAK~lVe~~P----~~iKe~v~keeAe~ik~kle~aG------a~ve 94 (96)
...|.|+|=+-+-..--.||..++.+ .|++..+|..+...+- .+|.. -++++|+.....|...| -.++
T Consensus 4 ~~~~~vvL~NDe~ht~~~Vi~~L~~~-~~~s~~~A~~~a~~v~~~G~avv~~-~~~e~ae~~~~~l~~~g~~~~~PL~~t 81 (82)
T PF02617_consen 4 PDMYRVVLWNDEVHTFEQVIDVLRRV-FGCSEEQARQIAMEVHREGRAVVGT-GSREEAEEYAEKLQRAGRDSGHPLRAT 81 (82)
T ss_dssp --EEEEEEE--SSSBHHHHHHHHHHH-C---HHHHHHHHHHHHHHSEEEEEE-EEHHHHHHHHHHHHHHHHHTT---EEE
T ss_pred CCceEEEEEcCCCCCHHHHHHHHHHH-HCCCHHHHHHHHHHHhHcCCEeeee-CCHHHHHHHHHHHHHHhhccCCCeEEe
Confidence 46789999776555677999999998 4999999998877553 45544 59999999999999998 6655
Q ss_pred e
Q psy4492 95 V 95 (96)
Q Consensus 95 i 95 (96)
|
T Consensus 82 i 82 (82)
T PF02617_consen 82 I 82 (82)
T ss_dssp E
T ss_pred C
Confidence 4
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 ....
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR
They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
