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Protein

SsrA-binding protein

Gene

smpB

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. 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 annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-216-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
SsrA-binding proteinUniRule annotation
Alternative name(s):
Small protein BUniRule annotation
Gene namesi
Name:smpBUniRule annotation
Synonyms:smb
Ordered Locus Names:aq_287
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

  • Note: The tmRNA-SmpB complex associates with stalled 70S ribosomes.UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 157157SsrA-binding proteinPRO_0000102894Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi224324.aq_287.

Structurei

Secondary structure

1
157
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 126Combined sources
Turni15 – 195Combined sources
Beta strandi22 – 276Combined sources
Helixi34 – 418Combined sources
Beta strandi48 – 569Combined sources
Beta strandi59 – 657Combined sources
Beta strandi84 – 863Combined sources
Helixi90 – 10314Combined sources
Beta strandi106 – 11712Combined sources
Beta strandi119 – 1268Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K8HNMR-A2-134[»]
1P6VX-ray3.20A/C2-157[»]
1ZC8electron microscopy13.00K2-131[»]
2OB7electron microscopy13.60B/C2-157[»]
ProteinModelPortaliO66640.
SMRiO66640. Positions 2-134.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO66640.

Family & Domainsi

Sequence similaritiesi

Belongs to the SmpB family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108UH4. Bacteria.
COG0691. LUCA.
HOGENOMiHOG000009628.
InParanoidiO66640.
KOiK03664.
OMAiQNKKASH.
OrthoDBiPOG091H022D.

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.

O66640-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKSDKIIPI AENKEAKAKY DILETYEAGI VLKGSEVKSL REKGTVSFKD
60 70 80 90 100
SFVRIENGEA WLYNLYIAPY KHATIENHDP LRKRKLLLHK REIMRLYGKV
110 120 130 140 150
QEKGYTIIPL KLYWKNNKVK VLIALAKGKK LYDRRRELKE KAMKRELERE

FKGKIHL
Length:157
Mass (Da):18,530
Last modified:August 1, 1998 - v1
Checksum:iFF43E3EF0FD77CFA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06597.1.
PIRiD70326.
RefSeqiNP_213200.1. NC_000918.1.
WP_010880138.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC06597; AAC06597; aq_287.
GeneIDi1192874.
KEGGiaae:aq_287.
PATRICi20958198. VBIAquAeo85532_0238.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06597.1.
PIRiD70326.
RefSeqiNP_213200.1. NC_000918.1.
WP_010880138.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1K8HNMR-A2-134[»]
1P6VX-ray3.20A/C2-157[»]
1ZC8electron microscopy13.00K2-131[»]
2OB7electron microscopy13.60B/C2-157[»]
ProteinModelPortaliO66640.
SMRiO66640. Positions 2-134.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_287.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC06597; AAC06597; aq_287.
GeneIDi1192874.
KEGGiaae:aq_287.
PATRICi20958198. VBIAquAeo85532_0238.

Phylogenomic databases

eggNOGiENOG4108UH4. Bacteria.
COG0691. LUCA.
HOGENOMiHOG000009628.
InParanoidiO66640.
KOiK03664.
OMAiQNKKASH.
OrthoDBiPOG091H022D.

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-216-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO66640.

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_AQUAE
AccessioniPrimary (citable) accession number: O66640
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: September 7, 2016
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Although the Valle et al., electron microscopy paper indicates this protein came from T.thermophilus its sequence maps to A.aeolicus.1 Publication

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.