SSRP_THET8
ID SSRP_THET8 Reviewed; 144 AA.
AC Q8RR57; Q5SMG1;
DT 23-APR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 25-MAY-2022, entry version 110.
DE RecName: Full=SsrA-binding protein {ECO:0000255|HAMAP-Rule:MF_00023};
DE AltName: Full=Small protein B {ECO:0000255|HAMAP-Rule:MF_00023};
GN Name=smpB {ECO:0000255|HAMAP-Rule:MF_00023}; OrderedLocusNames=TTHA0902;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Nameki N., Kimoto M., Terada T., Shirouzu M., Suetsugu-Hanawa K.,
RA Takaku H., Himeno H., Muto A., Inoue Y., Shibata T., Kuramitsu S.,
RA Yokoyama S., Kawai G.;
RT "Interaction of tmRNA with a tmRNA-binding protein, SmpB, from Thermus
RT thermophilus.";
RL Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP STRUCTURE BY NMR.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=12560085; DOI=10.1016/s0014-5793(02)03880-2;
RA Someya T., Nameki N., Hosoi H., Suzuki S., Hatanaka H., Fujii M.,
RA Terada T., Shirouzu M., Inoue Y., Shibata T., Kuramitsu S., Yokoyama S.,
RA Kawai G.;
RT "Solution structure of a tmRNA-binding protein, SmpB, from Thermus
RT thermophilus.";
RL FEBS Lett. 535:94-100(2003).
RN [4]
RP STRUCTURE BY ELECTRON MICROSCOPY (13.00 ANGSTROMS), FUNCTION, SUBUNIT,
RP RRNA-BINDING, AND TMRNA-BINDING.
RX PubMed=12677067; DOI=10.1126/science.1081798;
RA Valle M., Gillet R., Kaur S., Henne A., Ramakrishnan V., Frank J.;
RT "Visualizing tmRNA entry into a stalled ribosome.";
RL Science 300:127-130(2003).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-123 IN COMPLEX WITH TMRNA,
RP FUNCTION, SUBUNIT, AND TMRNA-BINDING.
RX PubMed=17488812; DOI=10.1073/pnas.0700402104;
RA Bessho Y., Shibata R., Sekine S., Murayama K., Higashijima K.,
RA Hori-Takemoto C., Shirouzu M., Kuramitsu S., Yokoyama S.;
RT "Structural basis for functional mimicry of long-variable-arm tRNA by
RT transfer-messenger RNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:8293-8298(2007).
RN [6]
RP STRUCTURE BY ELECTRON MICROSCOPY (13.00 ANGSTROMS) OF 2-144 IN COMPLEX WITH
RP TMRNA AND 70S RIBOSOMES, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION,
RP TMRNA-BINDING, AND RRNA-BINDING.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=20953161; DOI=10.1038/emboj.2010.252;
RA Weis F., Bron P., Giudice E., Rolland J.P., Thomas D., Felden B.,
RA Gillet R.;
RT "tmRNA-SmpB: a journey to the centre of the bacterial ribosome.";
RL EMBO J. 29:3810-3818(2010).
RN [7]
RP STRUCTURE BY ELECTRON MICROSCOPY (13.60 ANGSTROMS) OF 2-123 IN COMPLEX WITH
RP TMRNA AND 70S RIBOSOMES, FUNCTION, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=20940705; DOI=10.1038/emboj.2010.255;
RA Fu J., Hashem Y., Wower I., Lei J., Liao H.Y., Zwieb C., Wower J.,
RA Frank J.;
RT "Visualizing the transfer-messenger RNA as the ribosome resumes
RT translation.";
RL EMBO J. 29:3819-3825(2010).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS) IN COMPLEX WITH TMRNA AND 70S
RP RIBOSOMES, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, RRNA-BINDING, AND
RP TNRNA-BINDING.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=22422985; DOI=10.1126/science.1217039;
RA Neubauer C., Gillet R., Kelley A.C., Ramakrishnan V.;
RT "Decoding in the absence of a codon by tmRNA and SmpB in the ribosome.";
RL Science 335:1366-1369(2012).
RN [9]
RP STRUCTURE BY ELECTRON MICROSCOPY (8.30 ANGSTROMS) OF 1-123 IN COMPLEX WITH
RP TMRNA AND 70S RIBOSOMES, FUNCTION, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=22622583; DOI=10.1038/nature11006;
RA Ramrath D.J., Yamamoto H., Rother K., Wittek D., Pech M., Mielke T.,
RA Loerke J., Scheerer P., Ivanov P., Teraoka Y., Shpanchenko O.,
RA Nierhaus K.H., Spahn C.M.;
RT "The complex of tmRNA-SmpB and EF-G on translocating ribosomes.";
RL Nature 485:526-529(2012).
CC -!- FUNCTION: Required for rescue of stalled ribosomes mediated by trans-
CC translation. Binds to tmRNA (also known as SsrA and 10Sa), required for
CC stable association of tmRNA with ribosomes, probably by bridging tmRNA
CC to 50S subunit. tmRNA and SmpB together mimic tRNA shape, replacing the
CC anticodon stem-loop with SmpB (PubMed:22422985, PubMed:17488812). tmRNA
CC is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala)
CC and it encodes a 'tag peptide', a short internal open reading frame.
CC During trans-translation Ala-aminoacylated tmRNA acts like a tRNA,
CC entering the A-site of stalled ribosomes, displacing the stalled mRNA.
CC The ribosome then switches to translate the ORF on the tmRNA; the
CC nascent peptide is terminated with the 'tag peptide' encoded by the
CC tmRNA and targeted for degradation. The ribosome is freed to recommence
CC translation, which seems to be the essential function of trans-
CC translation. {ECO:0000255|HAMAP-Rule:MF_00023,
CC ECO:0000269|PubMed:12677067, ECO:0000269|PubMed:17488812,
CC ECO:0000269|PubMed:20940705, ECO:0000269|PubMed:20953161,
CC ECO:0000269|PubMed:22422985, ECO:0000269|PubMed:22622583}.
CC -!- SUBUNIT: Binds tmRNA (PubMed:12677067, PubMed:20953161,
CC PubMed:22422985, PubMed:17488812, PubMed:20940705, PubMed:22622583).
CC Binds to both the 50S and 30S ribosomal subunits via rRNA contacts,
CC bridges tmRNA binding to stalled ribosomes.
CC {ECO:0000269|PubMed:12677067, ECO:0000269|PubMed:17488812,
CC ECO:0000269|PubMed:20940705, ECO:0000269|PubMed:20953161,
CC ECO:0000269|PubMed:22422985, ECO:0000269|PubMed:22622583}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00023}.
CC Note=The tmRNA-SmpB complex associates with stalled 70S ribosomes
CC (PubMed:20953161, PubMed:22422985, PubMed:20940705, PubMed:22622583).
CC {ECO:0000255|HAMAP-Rule:MF_00023, ECO:0000269|PubMed:20940705,
CC ECO:0000269|PubMed:20953161, ECO:0000269|PubMed:22422985,
CC ECO:0000269|PubMed:22622583}.
CC -!- MISCELLANEOUS: Athough the Valle et al., electron microscopy paper
CC indicates this protein came from T.thermophilus, its sequence maps to
CC A.aeolicus (PubMed:12677067). The Fu et al., paper maps the coordinates
CC of T.thermophilus to E.coli (PubMed:20940705).
CC {ECO:0000305|PubMed:12677067, ECO:0000305|PubMed:20940705}.
CC -!- SIMILARITY: Belongs to the SmpB family. {ECO:0000255|HAMAP-
CC Rule:MF_00023}.
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DR EMBL; AB070601; BAB86918.1; -; Genomic_DNA.
DR EMBL; AP008226; BAD70725.1; -; Genomic_DNA.
DR RefSeq; WP_011172991.1; NC_006461.1.
DR RefSeq; YP_144168.1; NC_006461.1.
DR PDB; 1J1H; NMR; -; A=1-144.
DR PDB; 1WJX; X-ray; 1.70 A; A=2-123.
DR PDB; 2CZJ; X-ray; 3.01 A; A/C/E/G=1-123.
DR PDB; 3IYQ; EM; -; B=2-144.
DR PDB; 3IYR; EM; -; B=2-144.
DR PDB; 3IZ4; EM; -; B=2-123.
DR PDB; 4V6T; EM; 8.30 A; W=1-123.
DR PDB; 4V8Q; X-ray; 3.10 A; B2=1-144.
DR PDB; 6Q95; EM; 3.70 A; 5=1-144.
DR PDBsum; 1J1H; -.
DR PDBsum; 1WJX; -.
DR PDBsum; 2CZJ; -.
DR PDBsum; 3IYQ; -.
DR PDBsum; 3IYR; -.
DR PDBsum; 3IZ4; -.
DR PDBsum; 4V6T; -.
DR PDBsum; 4V8Q; -.
DR PDBsum; 6Q95; -.
DR AlphaFoldDB; Q8RR57; -.
DR SMR; Q8RR57; -.
DR STRING; 300852.55772284; -.
DR EnsemblBacteria; BAD70725; BAD70725; BAD70725.
DR GeneID; 3169917; -.
DR KEGG; ttj:TTHA0902; -.
DR PATRIC; fig|300852.9.peg.894; -.
DR eggNOG; COG0691; Bacteria.
DR HOGENOM; CLU_108953_0_0_0; -.
DR OMA; WTNHSAR; -.
DR PhylomeDB; Q8RR57; -.
DR EvolutionaryTrace; Q8RR57; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0070929; P:trans-translation; IEA:UniProtKB-UniRule.
DR CDD; cd09294; SmpB; 1.
DR Gene3D; 2.40.280.10; -; 1.
DR HAMAP; MF_00023; SmpB; 1.
DR InterPro; IPR023620; SmpB.
DR InterPro; IPR000037; SsrA-bd_prot.
DR InterPro; IPR020081; SsrA-bd_prot_CS.
DR PANTHER; PTHR30308; PTHR30308; 1.
DR Pfam; PF01668; SmpB; 1.
DR SUPFAM; SSF74982; SSF74982; 1.
DR TIGRFAMs; TIGR00086; smpB; 1.
DR PROSITE; PS01317; SSRP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Reference proteome; RNA-binding; rRNA-binding.
FT CHAIN 1..144
FT /note="SsrA-binding protein"
FT /id="PRO_0000103056"
FT HELIX 8..13
FT /evidence="ECO:0007829|PDB:1WJX"
FT STRAND 14..24
FT /evidence="ECO:0007829|PDB:1WJX"
FT HELIX 30..35
FT /evidence="ECO:0007829|PDB:1WJX"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:1WJX"
FT STRAND 52..57
FT /evidence="ECO:0007829|PDB:1WJX"
FT STRAND 60..63
FT /evidence="ECO:0007829|PDB:1J1H"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:1WJX"
FT HELIX 83..89
FT /evidence="ECO:0007829|PDB:1WJX"
FT TURN 90..92
FT /evidence="ECO:0007829|PDB:1WJX"
FT TURN 94..97
FT /evidence="ECO:0007829|PDB:1J1H"
FT STRAND 98..107
FT /evidence="ECO:0007829|PDB:1WJX"
FT TURN 109..111
FT /evidence="ECO:0007829|PDB:1J1H"
FT STRAND 113..122
FT /evidence="ECO:0007829|PDB:1WJX"
SQ SEQUENCE 144 AA; 16750 MW; 4691B4D48F1A2299 CRC64;
MAPVLENRRA RHDYEILETY EAGIALKGTE VKSLRAGKVD FTGSFARFED GELYLENLYI
APYEKGSYAN VDPRRKRKLL LHKHELRRLL GKVEQKGLTL VPLKIYFNER GYAKVLLGLA
RGKKAYEKRR EDKKEAVRRA LEEL
