SSRP_ECOLI
ID SSRP_ECOLI Reviewed; 160 AA.
AC P0A832; P32052; P77011;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 116.
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}; Synonyms=smqB;
GN OrderedLocusNames=b2620, JW2601;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=7524073; DOI=10.1073/pnas.91.20.9223;
RA Komine Y., Kitabatake M., Yokogawa T., Nishikawa K., Inokuchi H.;
RT "A tRNA-like structure is present in 10Sa RNA, a small stable RNA from
RT Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 91:9223-9227(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 2-16.
RC STRAIN=K12;
RX PubMed=2045357; DOI=10.1128/jb.173.11.3271-3272.1991;
RA Chauhan A.K., Miczak A., Apirion D.;
RT "Two new genes located between 2758 and 2761 kilobase pairs on the
RT Escherichia coli genome.";
RL J. Bacteriol. 173:3271-3272(1991).
RN [6]
RP PROTEIN SEQUENCE OF 2-8, FUNCTION, SUBCELLULAR LOCATION, DISRUPTION
RP PHENOTYPE, AND RNA-BINDING.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=10393194; DOI=10.1093/emboj/18.13.3793;
RA Karzai A.W., Susskind M.M., Sauer R.T.;
RT "SmpB, a unique RNA-binding protein essential for the peptide-tagging
RT activity of SsrA (tmRNA).";
RL EMBO J. 18:3793-3799(1999).
RN [7]
RP FUNCTION.
RX PubMed=11904185; DOI=10.1016/s0014-5793(02)02333-5;
RA Shimizu Y., Ueda T.;
RT "The role of SmpB protein in trans-translation.";
RL FEBS Lett. 514:74-77(2002).
RN [8]
RP FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, AND TMRNA-BINDING.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=11917023; DOI=10.1093/nar/30.7.1620;
RA Hanawa-Suetsugu K., Takagi M., Inokuchi H., Himeno H., Muto A.;
RT "SmpB functions in various steps of trans-translation.";
RL Nucleic Acids Res. 30:1620-1629(2002).
RN [9]
RP FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=15069072; DOI=10.1074/jbc.m314086200;
RA Hallier M., Ivanova N., Rametti A., Pavlov M., Ehrenberg M., Felden B.;
RT "Pre-binding of small protein B to a stalled ribosome triggers trans-
RT translation.";
RL J. Biol. Chem. 279:25978-25985(2004).
RN [10]
RP FUNCTION, SUBCELLULAR LOCATION, TMRNA-BINDING, AND MUTAGENESIS OF
RP 138-ASP--ARG-139; 138-LYS-ARG-139; ARG-139; 140-SER--ARG-160;
RP 152-ALA--ARG-160; 154-ILE-MET-155; 154-ILE--ARG-160; 155-MET--ARG-160 AND
RP 156-LYS--ARG-160.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=15699355; DOI=10.1073/pnas.0409694102;
RA Sundermeier T.R., Dulebohn D.P., Cho H.J., Karzai A.W.;
RT "A previously uncharacterized role for small protein B (SmpB) in transfer
RT messenger RNA-mediated trans-translation.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:2316-2321(2005).
RN [11]
RP FUNCTION, AND MUTAGENESIS OF TRP-147.
RX PubMed=20348441; DOI=10.1261/rna.1916610;
RA Kurita D., Muto A., Himeno H.;
RT "Role of the C-terminal tail of SmpB in the early stage of trans-
RT translation.";
RL RNA 16:980-990(2010).
RN [12]
RP FUNCTION, MODEL IN COMPLEX WITH TMRNA AND 70S RIBOSOMES, SUBUNIT, AND
RP 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 [13]
RP FUNCTION, MODEL IN COMPLEX WITH TMRNA AND 70S RIBOSOMES, SUBUNIT, AND
RP 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).
RN [14]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=23812681; DOI=10.1093/jac/dkt231;
RA Li J., Ji L., Shi W., Xie J., Zhang Y.;
RT "Trans-translation mediates tolerance to multiple antibiotics and stresses
RT in Escherichia coli.";
RL J. Antimicrob. Chemother. 68:2477-2481(2013).
CC -!- FUNCTION: Required for rescue of stalled ribosomes mediated by trans-
CC translation. Binds to tmRNA RNA (also known as SsrA or 10Sa RNA, 363
CC nucleotides in this organism), required for stable binding of tmRNA to
CC ribosomes (PubMed:10393194, PubMed:11904185, PubMed:11917023). tmRNA
CC and SmpB together mimic tRNA shape, replacing the anticodon stem-loop
CC with SmpB (Probable). tmRNA is encoded by the ssrA gene; the 2 termini
CC fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short
CC internal open reading frame. Able to recruit charged tmRNA to ribosomes
CC (PubMed:15069072). Does not play a role in transcription, processing or
CC Ala-aminoacylation of tmRNA (PubMed:10393194). Other studies have shown
CC it stimulates aminoacylation of tmRNA (PubMed:11917023,
CC PubMed:11904185). May protect tmRNA from degradation (PubMed:11917023).
CC Binds to tmRNA that cannot be aminoacylated (tmRNA G3A), does not bind
CC to tmRNA mutations near the tRNA-like termini (tmRNA G19C, A334U);
CC other tmRNA mutations that block trans-translation still bind SmpB
CC (PubMed:11917023). With tmRNA may play a role in bacterial persistence
CC (PubMed:23812681). During trans-translation Ala-aminoacylated transfer-
CC messenger RNA acts like a tRNA, entering the A-site of stalled
CC ribosomes, displacing the stalled mRNA. The ribosome then switches to
CC translate the ORF on the tmRNA, the nascent peptide is terminated with
CC the 'tag peptide' encoded by the tmRNA and targeted for degradation.
CC The ribosome is freed to recommence translation, which seems to be the
CC essential function of trans-translation. {ECO:0000269|PubMed:10393194,
CC ECO:0000269|PubMed:11904185, ECO:0000269|PubMed:11917023,
CC ECO:0000269|PubMed:15069072, ECO:0000269|PubMed:15699355,
CC ECO:0000269|PubMed:20348441, ECO:0000269|PubMed:20940705,
CC ECO:0000269|PubMed:22622583, ECO:0000269|PubMed:23812681,
CC ECO:0000305|PubMed:20940705}.
CC -!- SUBUNIT: Binds tmRNA (PubMed:10393194, PubMed:11904185,
CC PubMed:11917023, PubMed:15699355, PubMed:20940705, PubMed:22622583).
CC The SmpB-tmRNA complex binds to stalled ribosomes (PubMed:10393194,
CC PubMed:11917023, PubMed:15699355, PubMed:20940705, PubMed:22622583).
CC {ECO:0000269|PubMed:10393194, ECO:0000269|PubMed:11904185,
CC ECO:0000269|PubMed:11917023, ECO:0000269|PubMed:15069072,
CC ECO:0000269|PubMed:15699355, ECO:0000269|PubMed:20940705,
CC ECO:0000269|PubMed:22622583}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00023,
CC ECO:0000269|PubMed:11917023, ECO:0000269|PubMed:15069072}. Note=The
CC tmRNA-SmpB complex associates with stalled ribosomes (PubMed:10393194,
CC PubMed:11917023, PubMed:15699355, PubMed:20940705, PubMed:22622583).
CC SmpB associates with ribosomes even in the absence of tmRNA
CC (PubMed:15069072). {ECO:0000255|HAMAP-Rule:MF_00023,
CC ECO:0000269|PubMed:10393194, ECO:0000269|PubMed:11917023,
CC ECO:0000269|PubMed:15069072, ECO:0000269|PubMed:15699355,
CC ECO:0000269|PubMed:20940705, ECO:0000269|PubMed:22622583}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype during growth on solid
CC medium at 16-42 degrees Celsius on rich or minimal media, no peptide-
CC tagging of proteins translated from mRNA lacking a stop codon by tmRNA,
CC i.e. no trans-translation (PubMed:10393194, PubMed:11917023,
CC PubMed:15069072). 4-8 fold increased susceptibility to a number of
CC antibiotics (norfloxacin, gentamicin, trimethoprim, tetracycline and
CC streptomycin but not ampicillin), very significantly reduced production
CC of persister cells (PubMed:23812681). A number of bacteriophage
CC development defects (PubMed:10393194). {ECO:0000269|PubMed:10393194,
CC ECO:0000269|PubMed:11917023, ECO:0000269|PubMed:15069072,
CC ECO:0000269|PubMed:23812681}.
CC -!- MISCELLANEOUS: Although the Fu et al., electron microscopy paper
CC indicates this protein came from E.coli its sequence maps to
CC T.thermophilus (PubMed:20940705). The same situation holds for Ramrath
CC et al., (PubMed:22622583). {ECO:0000305|PubMed:20940705,
CC ECO:0000305|PubMed:22622583}.
CC -!- SIMILARITY: Belongs to the SmpB family. {ECO:0000255|HAMAP-
CC Rule:MF_00023}.
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DR EMBL; D12501; BAA02062.1; -; Genomic_DNA.
DR EMBL; U36840; AAA79790.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75669.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16505.2; -; Genomic_DNA.
DR PIR; JS0701; JS0701.
DR RefSeq; NP_417110.1; NC_000913.3.
DR RefSeq; WP_000162574.1; NZ_STEB01000040.1.
DR PDB; 6Q97; EM; 3.90 A; 5=14-158.
DR PDB; 6Q9A; EM; 3.70 A; 5=14-131.
DR PDB; 7ABZ; EM; 3.21 A; 5=14-159.
DR PDB; 7AC7; EM; 3.08 A; 5=14-160.
DR PDB; 7ACJ; EM; 3.20 A; 5=11-160.
DR PDBsum; 6Q97; -.
DR PDBsum; 6Q9A; -.
DR PDBsum; 7ABZ; -.
DR PDBsum; 7AC7; -.
DR PDBsum; 7ACJ; -.
DR AlphaFoldDB; P0A832; -.
DR SMR; P0A832; -.
DR BioGRID; 4260987; 42.
DR BioGRID; 851624; 1.
DR DIP; DIP-47871N; -.
DR IntAct; P0A832; 32.
DR STRING; 511145.b2620; -.
DR jPOST; P0A832; -.
DR PaxDb; P0A832; -.
DR PRIDE; P0A832; -.
DR EnsemblBacteria; AAC75669; AAC75669; b2620.
DR EnsemblBacteria; BAA16505; BAA16505; BAA16505.
DR GeneID; 67414063; -.
DR GeneID; 947296; -.
DR KEGG; ecj:JW2601; -.
DR KEGG; eco:b2620; -.
DR PATRIC; fig|1411691.4.peg.4119; -.
DR EchoBASE; EB1730; -.
DR eggNOG; COG0691; Bacteria.
DR HOGENOM; CLU_108953_3_0_6; -.
DR InParanoid; P0A832; -.
DR OMA; WTNHSAR; -.
DR PhylomeDB; P0A832; -.
DR BioCyc; EcoCyc:EG11782-MON; -.
DR PRO; PR:P0A832; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IDA:EcoCyc.
DR GO; GO:0070929; P:trans-translation; IEA:UniProtKB-UniRule.
DR GO; GO:0070930; P:trans-translation-dependent protein tagging; IMP:EcoCyc.
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; Direct protein sequencing; Reference proteome;
KW RNA-binding.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10393194,
FT ECO:0000269|PubMed:2045357"
FT CHAIN 2..160
FT /note="SsrA-binding protein"
FT /id="PRO_0000102944"
FT MUTAGEN 137..139
FT /note="DKR->AAA: Almost complete loss of protein tagging by
FT trans-translation, binds tmRNA normally, binds ribosomes
FT normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 138..139
FT /note="KR->AA: About half loss of protein tagging by trans-
FT translation, binds tmRNA normally, binds ribosomes
FT normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 139
FT /note="R->E: About half loss of protein tagging by trans-
FT translation, binds tmRNA normally, binds ribosomes
FT normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 140..160
FT /note="Missing: Complete loss of protein tagging by trans-
FT translation, binds tmRNA normally, binds ribosomes
FT normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 147
FT /note="W->C,D: 70% loss of tagging by trans-translation,
FT binds tmRNA normally."
FT /evidence="ECO:0000269|PubMed:20348441"
FT MUTAGEN 147
FT /note="W->K: 97% loss of tagging by trans-translation,
FT binds tmRNA normally, altered binding of the tmRNA-SmpB
FT complex in the ribosomes A-site."
FT /evidence="ECO:0000269|PubMed:20348441"
FT MUTAGEN 152..160
FT /note="Missing: Complete loss of protein tagging by trans-
FT translation, binds ribosomes normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 154..160
FT /note="Missing: Almost complete loss of protein tagging by
FT trans-translation, binds tmRNA normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 154..155
FT /note="IM->AA: Decreased protein tagging by trans-
FT translation, binds ribosomes normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 154..155
FT /note="IM->DE: Loss of protein tagging by trans-
FT translation, binds tmRNA and ribosomes normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 154..155
FT /note="IM->LI,RK,QQ: No effect on protein tagging by trans-
FT translation."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 155..160
FT /note="Missing: Slightly increased protein tagging by
FT trans-translation, binds ribosomes normally."
FT /evidence="ECO:0000269|PubMed:15699355"
FT MUTAGEN 156..160
FT /note="Missing: No effect on protein tagging by trans-
FT translation, binds ribosomes normally."
FT /evidence="ECO:0000269|PubMed:15699355"
SQ SEQUENCE 160 AA; 18269 MW; F7E45A16540EA300 CRC64;
MTKKKAHKPG SATIALNKRA RHEYFIEEEF EAGLALQGWE VKSLRAGKAN ISDSYVLLRD
GEAFLFGANI TPMAVASTHV VCDPTRTRKL LLNQRELDSL YGRVNREGYT VVALSLYWKN
AWCKVKIGVA KGKKQHDKRS DIKEREWQVD KARIMKNAHR
