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Protein

SsrA-binding protein

Gene

smpB

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Required for rescue of stalled ribosomes mediated by trans-translation. Binds to tmRNA (also known as SsrA and 10Sa), required for stable association of tmRNA with ribosomes, probably by bridging tmRNA to 50S subunit. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB (PubMed:22422985, PubMed:17488812). tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation.UniRule annotation6 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-935-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
SsrA-binding proteinUniRule annotation
Alternative name(s):
Small protein BUniRule annotation
Gene namesi
Name:smpBUniRule annotation
Ordered Locus Names:TTHA0902
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000532 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 144144SsrA-binding proteinPRO_0000103056Add
BLAST

Interactioni

Subunit structurei

Binds tmRNA (PubMed:12677067, PubMed:20953161, PubMed:22422985, PubMed:17488812, PubMed:20940705, PubMed:22622583). Binds to both the 50S and 30S ribosomal subunits via rRNA contacts, bridges tmRNA binding to stalled ribosomes.6 Publications

Protein-protein interaction databases

STRINGi300852.TTHA0902.

Structurei

Secondary structure

1
144
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi8 – 136Combined sources
Beta strandi14 – 2411Combined sources
Helixi30 – 356Combined sources
Beta strandi45 – 495Combined sources
Beta strandi52 – 576Combined sources
Beta strandi60 – 634Combined sources
Beta strandi77 – 804Combined sources
Helixi83 – 897Combined sources
Turni90 – 923Combined sources
Turni94 – 974Combined sources
Beta strandi98 – 10710Combined sources
Turni109 – 1113Combined sources
Beta strandi113 – 12210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J1HNMR-A1-144[»]
1WJXX-ray1.70A2-123[»]
2CZJX-ray3.01A/C/E/G1-123[»]
3IYQelectron microscopy-B2-144[»]
3IYRelectron microscopy-B2-144[»]
3IZ4electron microscopy-B2-123[»]
4V6Telectron microscopy8.30W1-123[»]
4V8QX-ray3.10B21-144[»]
ProteinModelPortaliQ8RR57.
SMRiQ8RR57. Positions 1-123.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8RR57.

Family & Domainsi

Sequence similaritiesi

Belongs to the SmpB family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108UH4. Bacteria.
COG0691. LUCA.
HOGENOMiHOG000009628.
KOiK03664.
OMAiYTNHDPR.
OrthoDBiEOG6HXJ9P.
PhylomeDBiQ8RR57.

Family and domain databases

Gene3Di2.40.280.10. 1 hit.
HAMAPiMF_00023. SmpB.
InterProiIPR023620. SmpB.
IPR000037. SsrA-bd_prot.
IPR020081. SsrA-bd_prot_CS.
[Graphical view]
PfamiPF01668. SmpB. 1 hit.
[Graphical view]
ProDomiPD004488. SmpB. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF74982. SSF74982. 1 hit.
TIGRFAMsiTIGR00086. smpB. 1 hit.
PROSITEiPS01317. SSRP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8RR57-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPVLENRRA RHDYEILETY EAGIALKGTE VKSLRAGKVD FTGSFARFED
60 70 80 90 100
GELYLENLYI APYEKGSYAN VDPRRKRKLL LHKHELRRLL GKVEQKGLTL
110 120 130 140
VPLKIYFNER GYAKVLLGLA RGKKAYEKRR EDKKEAVRRA LEEL
Length:144
Mass (Da):16,750
Last modified:June 1, 2002 - v1
Checksum:i4691B4D48F1A2299
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB070601 Genomic DNA. Translation: BAB86918.1.
AP008226 Genomic DNA. Translation: BAD70725.1.
RefSeqiWP_011172991.1. NC_006461.1.
YP_144168.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD70725; BAD70725; BAD70725.
GeneIDi3169917.
KEGGittj:TTHA0902.
PATRICi23956784. VBITheThe93045_0894.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB070601 Genomic DNA. Translation: BAB86918.1.
AP008226 Genomic DNA. Translation: BAD70725.1.
RefSeqiWP_011172991.1. NC_006461.1.
YP_144168.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J1HNMR-A1-144[»]
1WJXX-ray1.70A2-123[»]
2CZJX-ray3.01A/C/E/G1-123[»]
3IYQelectron microscopy-B2-144[»]
3IYRelectron microscopy-B2-144[»]
3IZ4electron microscopy-B2-123[»]
4V6Telectron microscopy8.30W1-123[»]
4V8QX-ray3.10B21-144[»]
ProteinModelPortaliQ8RR57.
SMRiQ8RR57. Positions 1-123.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA0902.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD70725; BAD70725; BAD70725.
GeneIDi3169917.
KEGGittj:TTHA0902.
PATRICi23956784. VBITheThe93045_0894.

Phylogenomic databases

eggNOGiENOG4108UH4. Bacteria.
COG0691. LUCA.
HOGENOMiHOG000009628.
KOiK03664.
OMAiYTNHDPR.
OrthoDBiEOG6HXJ9P.
PhylomeDBiQ8RR57.

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-935-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ8RR57.

Family and domain databases

Gene3Di2.40.280.10. 1 hit.
HAMAPiMF_00023. SmpB.
InterProiIPR023620. SmpB.
IPR000037. SsrA-bd_prot.
IPR020081. SsrA-bd_prot_CS.
[Graphical view]
PfamiPF01668. SmpB. 1 hit.
[Graphical view]
ProDomiPD004488. SmpB. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF74982. SSF74982. 1 hit.
TIGRFAMsiTIGR00086. smpB. 1 hit.
PROSITEiPS01317. SSRP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Interaction of tmRNA with a tmRNA-binding protein, SmpB, from Thermus thermophilus."
    Nameki N., Kimoto M., Terada T., Shirouzu M., Suetsugu-Hanawa K., Takaku H., Himeno H., Muto A., Inoue Y., Shibata T., Kuramitsu S., Yokoyama S., Kawai G.
    Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  3. Cited for: STRUCTURE BY NMR.
    Strain: HB8 / ATCC 27634 / DSM 579.
  4. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (13.00 ANGSTROMS), FUNCTION, SUBUNIT, RRNA-BINDING, TMRNA-BINDING.
  5. "Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA."
    Bessho Y., Shibata R., Sekine S., Murayama K., Higashijima K., Hori-Takemoto C., Shirouzu M., Kuramitsu S., Yokoyama S.
    Proc. Natl. Acad. Sci. U.S.A. 104:8293-8298(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-123 IN COMPLEX WITH TMRNA, FUNCTION, SUBUNIT, TMRNA-BINDING.
  6. "tmRNA-SmpB: a journey to the centre of the bacterial ribosome."
    Weis F., Bron P., Giudice E., Rolland J.P., Thomas D., Felden B., Gillet R.
    EMBO J. 29:3810-3818(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY ELECTRON MICROSCOPY (13.00 ANGSTROMS) OF 2-144 IN COMPLEX WITH TMRNA AND 70S RIBOSOMES, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, TMRNA-BINDING, RRNA-BINDING.
    Strain: HB8 / ATCC 27634 / DSM 579.
  7. "Visualizing the transfer-messenger RNA as the ribosome resumes translation."
    Fu J., Hashem Y., Wower I., Lei J., Liao H.Y., Zwieb C., Wower J., Frank J.
    EMBO J. 29:3819-3825(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY ELECTRON MICROSCOPY (13.60 ANGSTROMS) OF 2-123 IN COMPLEX WITH TMRNA AND 70S RIBOSOMES, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION.
  8. "Decoding in the absence of a codon by tmRNA and SmpB in the ribosome."
    Neubauer C., Gillet R., Kelley A.C., Ramakrishnan V.
    Science 335:1366-1369(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS) IN COMPLEX WITH TMRNA AND 70S RIBOSOMES, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, RRNA-BINDING, TNRNA-BINDING.
    Strain: HB8 / ATCC 27634 / DSM 579.
  9. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (8.30 ANGSTROMS) OF 1-123 IN COMPLEX WITH TMRNA AND 70S RIBOSOMES, FUNCTION, SUBUNIT, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiSSRP_THET8
AccessioniPrimary (citable) accession number: Q8RR57
Secondary accession number(s): Q5SMG1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: June 1, 2002
Last modified: November 11, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Athough the Valle et al., electron microscopy paper indicates this protein came from T.thermophilus, its sequence maps to A.aeolicus (PubMed:12677067). The Fu et al., paper maps the coordinates of T.thermophilus to E.coli (PubMed:20940705).2 Publications

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.