Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

mRNA interferase YafQ

Gene

yafQ

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

Functioni

Toxic component of a toxin-antitoxin (TA) module. A sequence-specific mRNA endoribonuclease that inhibits translation elongation and induces bacterial stasis. Cleavage occurs between the second and third residue of the Lys codon followed by a G or A (5'AAA(G/A)3'), is reading-frame dependent and occurs within the 5' end of most mRNAs. Ribosome-binding confers the sequence specificity and reading frame-dependence. When overexpressed in liquid media YafQ partially inhibits protein synthesis, with a reduction in growth rate and colony growth rate. This effect is counteracted by coexpression with DinJ, the YafQ antitoxin. YafQ and DinJ together bind their own promoter, and by analogy to other TA modules probably repress its expression.
Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei87 – 871Proton donorCurated

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • endoribonuclease activity Source: EcoCyc
  • endoribonuclease activity, producing 3'-phosphomonoesters Source: EcoCyc
  • ribosome binding Source: EcoCyc
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • mRNA catabolic process Source: EcoCyc
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • response to antibiotic Source: EcoCyc
  • single-species biofilm formation Source: EcoCyc
  • transcription, DNA-templated Source: UniProtKB-KW
  • translational termination Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Repressor, Toxin

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6109-MONOMER.
ECOL316407:JW0215-MONOMER.
MetaCyc:G6109-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
mRNA interferase YafQ (EC:3.1.-.-)
Alternative name(s):
Endoribonuclease YafQ
Toxin YafQ
Gene namesi
Name:yafQ
Ordered Locus Names:b0225, JW0215
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13154. yafQ.

Pathology & Biotechi

Disruption phenotypei

Cells missing yafQ show increased biofilm sensitivity to the antibiotics cefazolin (a beta-lactam inhibitor) and tobramycin (a protein synthesis inhibitor). There is no difference in antibiotic sensitivity in stationary phase planktonic cells. Cells missing dinJ-yafQ have reduced biofilm formation.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi87 – 871H → Q: Loss of mRNA cleavage, loss of toxic effect. Still associates with the ribosome. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9292mRNA interferase YafQPRO_0000168540Add
BLAST

Proteomic databases

PaxDbiQ47149.

Expressioni

Developmental stagei

May function as a drug tolerance determinant in biofilm, but not stationary phase planktonic cells.1 Publication

Inductioni

By the DNA damaging agent mitomycin C.1 Publication

Gene expression databases

CollecTFiEXPREG_00000de0.

Interactioni

Subunit structurei

Forms a complex with antitoxin DinJ, possibly a heterotetramer. In this complex the toxin activity is inhibited. Binds the 70S ribosome via the 50S ribosomal subunit.2 Publications

Protein-protein interaction databases

BioGridi4259771. 15 interactions.
DIPiDIP-11221N.
IntActiQ47149. 4 interactions.
MINTiMINT-1263057.
STRINGi511145.b0225.

Structurei

Secondary structure

1
92
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Helixi10 – 2112Combined sources
Helixi26 – 3712Combined sources
Helixi45 – 473Combined sources
Helixi54 – 563Combined sources
Beta strandi60 – 656Combined sources
Beta strandi68 – 747Combined sources
Beta strandi76 – 8510Combined sources
Helixi87 – 915Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4ML2X-ray1.50A1-92[»]
4MMGX-ray1.50A/B1-92[»]
4Q2UX-ray1.80B/D/F/H/J/L/N/P2-92[»]
ProteinModelPortaliQ47149.
SMRiQ47149. Positions 2-92.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

To H.influenzae HI_0711.Curated

Phylogenomic databases

eggNOGiENOG4105VXN. Bacteria.
COG3041. LUCA.
HOGENOMiHOG000062216.
InParanoidiQ47149.
KOiK19157.
OMAiHRECHIQ.
PhylomeDBiQ47149.

Family and domain databases

InterProiIPR007712. RelE/ParE_toxin.
IPR004386. Toxin_YafQ-like.
[Graphical view]
PfamiPF15738. YafQ_toxin. 1 hit.
[Graphical view]
PIRSFiPIRSF006156. YafQ. 1 hit.
TIGRFAMsiTIGR02385. RelE_StbE. 1 hit.
TIGR00053. TIGR00053. 1 hit.

Sequencei

Sequence statusi: Complete.

Q47149-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIQRDIEYSG QYSKDVKLAQ KRHKDMNKLK YLMTLLINNT LPLPAVYKDH
60 70 80 90
PLQGSWKGYR DAHVEPDWIL IYKLTDKLLR FERTGTHAAL FG
Length:92
Mass (Da):10,847
Last modified:November 1, 1997 - v1
Checksum:i6EF6BD97C7F74291
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D38582 Genomic DNA. Translation: BAA07587.1.
U00096 Genomic DNA. Translation: AAC73329.1.
AP009048 Genomic DNA. Translation: BAA77895.1.
PIRiB64747.
RefSeqiNP_414760.1. NC_000913.3.
WP_000615983.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73329; AAC73329; b0225.
BAA77895; BAA77895; BAA77895.
GeneIDi944911.
KEGGiecj:JW0215.
eco:b0225.
PATRICi32115565. VBIEscCol129921_0227.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D38582 Genomic DNA. Translation: BAA07587.1.
U00096 Genomic DNA. Translation: AAC73329.1.
AP009048 Genomic DNA. Translation: BAA77895.1.
PIRiB64747.
RefSeqiNP_414760.1. NC_000913.3.
WP_000615983.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4ML2X-ray1.50A1-92[»]
4MMGX-ray1.50A/B1-92[»]
4Q2UX-ray1.80B/D/F/H/J/L/N/P2-92[»]
ProteinModelPortaliQ47149.
SMRiQ47149. Positions 2-92.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259771. 15 interactions.
DIPiDIP-11221N.
IntActiQ47149. 4 interactions.
MINTiMINT-1263057.
STRINGi511145.b0225.

Proteomic databases

PaxDbiQ47149.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73329; AAC73329; b0225.
BAA77895; BAA77895; BAA77895.
GeneIDi944911.
KEGGiecj:JW0215.
eco:b0225.
PATRICi32115565. VBIEscCol129921_0227.

Organism-specific databases

EchoBASEiEB2948.
EcoGeneiEG13154. yafQ.

Phylogenomic databases

eggNOGiENOG4105VXN. Bacteria.
COG3041. LUCA.
HOGENOMiHOG000062216.
InParanoidiQ47149.
KOiK19157.
OMAiHRECHIQ.
PhylomeDBiQ47149.

Enzyme and pathway databases

BioCyciEcoCyc:G6109-MONOMER.
ECOL316407:JW0215-MONOMER.
MetaCyc:G6109-MONOMER.

Miscellaneous databases

PROiQ47149.

Gene expression databases

CollecTFiEXPREG_00000de0.

Family and domain databases

InterProiIPR007712. RelE/ParE_toxin.
IPR004386. Toxin_YafQ-like.
[Graphical view]
PfamiPF15738. YafQ_toxin. 1 hit.
[Graphical view]
PIRSFiPIRSF006156. YafQ. 1 hit.
TIGRFAMsiTIGR02385. RelE_StbE. 1 hit.
TIGR00053. TIGR00053. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYAFQ_ECOLI
AccessioniPrimary (citable) accession number: Q47149
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: September 7, 2016
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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.