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Protein

SsrA-binding protein

Gene

smpB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required for rescue of stalled ribosomes mediated by trans-translation. Binds to tmRNA RNA (also known as SsrA or 10Sa RNA, 363 nucleotides in this organism), required for stable binding of tmRNA to ribosomes (PubMed:10393194, PubMed:11904185, PubMed:11917023). tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB (Probable). 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. Able to recruit charged tmRNA to ribosomes (PubMed:15069072). Does not play a role in transcription, processing or Ala-aminoacylation of tmRNA (PubMed:10393194). Other studies have shown it stimulates aminoacylation of tmRNA (PubMed:11917023, PubMed:11904185). May protect tmRNA from degradation (PubMed:11917023). Binds to tmRNA that cannot be aminoacylated (tmRNA G3A), does not bind to tmRNA mutations near the tRNA-like termini (tmRNA G19C, A334U); other tmRNA mutations that block trans-translation still bind SmpB (PubMed:11917023). With tmRNA may play a role in bacterial persistence (PubMed:23812681). During trans-translation Ala-aminoacylated transfer-messenger RNA 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.1 Publication9 Publications

GO - Molecular functioni

  • RNA binding Source: EcoCyc

GO - Biological processi

  • trans-translation Source: UniProtKB-HAMAP
  • trans-translation-dependent protein tagging Source: EcoCyc
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11782-MONOMER.
ECOL316407:JW2601-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
SsrA-binding proteinUniRule annotation
Alternative name(s):
Small protein BUniRule annotation
Gene namesi
Name:smpBUniRule annotation
Synonyms:smqB
Ordered Locus Names:b2620, JW2601
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11782. smpB.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

No visible phenotype during growth on solid medium at 16-42 degrees Celsius on rich or minimal media, no peptide-tagging of proteins translated from mRNA lacking a stop codon by tmRNA, i.e. no trans-translation (PubMed:10393194, PubMed:11917023, PubMed:15069072). 4-8 fold increased susceptibility to a number of antibiotics (norfloxacin, gentamicin, trimethoprim, tetracycline and streptomycin but not ampicillin), very significantly reduced production of persister cells (PubMed:23812681). A number of bacteriophage development defects (PubMed:10393194).4 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi137 – 1393DKR → AAA: Almost complete loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 Publication
Mutagenesisi138 – 1392KR → AA: About half loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 Publication
Mutagenesisi139 – 1391R → E: About half loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 Publication
Mutagenesisi140 – 16021Missing : Complete loss of protein tagging by trans-translation, binds tmRNA normally, binds ribosomes normally. 1 PublicationAdd
BLAST
Mutagenesisi147 – 1471W → C or D: 70% loss of tagging by trans-translation, binds tmRNA normally. 1 Publication
Mutagenesisi147 – 1471W → K: 97% loss of tagging by trans-translation, binds tmRNA normally, altered binding of the tmRNA-SmpB complex in the ribosomes A-site. 1 Publication
Mutagenesisi152 – 1609Missing : Complete loss of protein tagging by trans-translation, binds ribosomes normally. 1 Publication
Mutagenesisi154 – 1607Missing : Almost complete loss of protein tagging by trans-translation, binds tmRNA normally. 1 Publication
Mutagenesisi154 – 1552IM → AA: Decreased protein tagging by trans-translation, binds ribosomes normally. 1 Publication
Mutagenesisi154 – 1552IM → DE: Loss of protein tagging by trans-translation, binds tmRNA and ribosomes normally. 1 Publication
Mutagenesisi154 – 1552IM → LI, RK or QQ: No effect on protein tagging by trans-translation. 1 Publication
Mutagenesisi155 – 1606Missing : Slightly increased protein tagging by trans-translation, binds ribosomes normally. 1 Publication
Mutagenesisi156 – 1605Missing : No effect on protein tagging by trans-translation, binds ribosomes normally. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 160159SsrA-binding proteinPRO_0000102944Add
BLAST

Proteomic databases

PaxDbiP0A832.
PRIDEiP0A832.

Interactioni

Subunit structurei

Binds tmRNA (PubMed:10393194, PubMed:11904185, PubMed:11917023, PubMed:15699355, PubMed:20940705, PubMed:22622583). The SmpB-tmRNA complex binds to stalled ribosomes (PubMed:10393194, PubMed:11917023, PubMed:15699355, PubMed:20940705, PubMed:22622583).7 Publications

Protein-protein interaction databases

BioGridi4260987. 26 interactions.
DIPiDIP-47871N.
IntActiP0A832. 32 interactions.
MINTiMINT-1229819.
STRINGi511145.b2620.

Structurei

3D structure databases

ProteinModelPortaliP0A832.
SMRiP0A832. Positions 14-134.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the SmpB family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108UH4. Bacteria.
COG0691. LUCA.
HOGENOMiHOG000009628.
InParanoidiP0A832.
KOiK03664.
OMAiQNKKASH.
PhylomeDBiP0A832.

Family and domain databases

CDDicd09294. SmpB. 1 hit.
Gene3Di2.40.280.10. 1 hit.
HAMAPiMF_00023. SmpB. 1 hit.
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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A832-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKKKAHKPG SATIALNKRA RHEYFIEEEF EAGLALQGWE VKSLRAGKAN
60 70 80 90 100
ISDSYVLLRD GEAFLFGANI TPMAVASTHV VCDPTRTRKL LLNQRELDSL
110 120 130 140 150
YGRVNREGYT VVALSLYWKN AWCKVKIGVA KGKKQHDKRS DIKEREWQVD
160
KARIMKNAHR
Length:160
Mass (Da):18,269
Last modified:January 23, 2007 - v2
Checksum:iF7E45A16540EA300
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12501 Genomic DNA. Translation: BAA02062.1.
U36840 Genomic DNA. Translation: AAA79790.1.
U00096 Genomic DNA. Translation: AAC75669.1.
AP009048 Genomic DNA. Translation: BAA16505.2.
PIRiJS0701.
RefSeqiNP_417110.1. NC_000913.3.
WP_000162574.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75669; AAC75669; b2620.
BAA16505; BAA16505; BAA16505.
GeneIDi947296.
KEGGiecj:JW2601.
eco:b2620.
PATRICi32120639. VBIEscCol129921_2718.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12501 Genomic DNA. Translation: BAA02062.1.
U36840 Genomic DNA. Translation: AAA79790.1.
U00096 Genomic DNA. Translation: AAC75669.1.
AP009048 Genomic DNA. Translation: BAA16505.2.
PIRiJS0701.
RefSeqiNP_417110.1. NC_000913.3.
WP_000162574.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0A832.
SMRiP0A832. Positions 14-134.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260987. 26 interactions.
DIPiDIP-47871N.
IntActiP0A832. 32 interactions.
MINTiMINT-1229819.
STRINGi511145.b2620.

Proteomic databases

PaxDbiP0A832.
PRIDEiP0A832.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75669; AAC75669; b2620.
BAA16505; BAA16505; BAA16505.
GeneIDi947296.
KEGGiecj:JW2601.
eco:b2620.
PATRICi32120639. VBIEscCol129921_2718.

Organism-specific databases

EchoBASEiEB1730.
EcoGeneiEG11782. smpB.

Phylogenomic databases

eggNOGiENOG4108UH4. Bacteria.
COG0691. LUCA.
HOGENOMiHOG000009628.
InParanoidiP0A832.
KOiK03664.
OMAiQNKKASH.
PhylomeDBiP0A832.

Enzyme and pathway databases

BioCyciEcoCyc:EG11782-MONOMER.
ECOL316407:JW2601-MONOMER.

Miscellaneous databases

PROiP0A832.

Family and domain databases

CDDicd09294. SmpB. 1 hit.
Gene3Di2.40.280.10. 1 hit.
HAMAPiMF_00023. SmpB. 1 hit.
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...

Entry informationi

Entry nameiSSRP_ECOLI
AccessioniPrimary (citable) accession number: P0A832
Secondary accession number(s): P32052, P77011
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 85 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Although the Fu et al., electron microscopy paper indicates this protein came from E.coli its sequence maps to T.thermophilus (PubMed:20940705). The same situation holds for Ramrath et al., (PubMed:22622583).2 Publications

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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.