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Protein

mRNA interferase toxin 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 type II toxin-antitoxin (TA) module (PubMed:17263853). A sequence-specific mRNA endoribonuclease that inhibits translation elongation and induces bacterial stasis (PubMed:19210620). 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 (PubMed:19210620). Ribosome-binding confers the sequence specificity and reading frame-dependence (PubMed:19210620). 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 cognate antitoxin DinJ (PubMed:17263853). YafQ and DinJ together bind their own promoter, and repress its expression (PubMed:24898247).3 Publications
Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation (PubMed:19707553). mRNA interferases play a role in bacterial persistence to antibiotics (PubMed:21788497).2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei87Proton donorCurated1

GO - Molecular functioni

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

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

Keywordsi

Molecular functionDNA-binding, Endonuclease, Hydrolase, Nuclease, Repressor, RNA-binding, Toxin
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyciEcoCyc:G6109-MONOMER.
MetaCyc:G6109-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
mRNA interferase toxin 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13154. yafQ.

Subcellular locationi

GO - Cellular componenti

  • protein-DNA complex Source: CollecTF

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 (PubMed:19307375). Cells missing dinJ-yafQ have reduced biofilm formation. mRNA interferases play a role in bacterial persistence to antibiotics; as 10 mRNA interferases are successively deleted reduced levels of persisters are generated (PubMed:21788497).3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi87H → Q: Loss of mRNA cleavage, loss of toxic effect. Still associates with the ribosome. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001685401 – 92mRNA interferase toxin YafQAdd BLAST92

Proteomic databases

PaxDbiQ47149.
PRIDEiQ47149.

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

Monomer in the absence of antitoxin (PubMed:24898247). Forms a heterotetramer with antitoxin DinJ, with 2 YafQ-DinJ dimers associated via the N-terminus of the DinJ antitoxins (YafQ-(DinJ)2-YafQ) (PubMed:17263853, PubMed:24898247). In this complex the toxin activity is inhibited. Binds the 70S ribosome via the 50S ribosomal subunit (PubMed:19210620).3 Publications

Protein-protein interaction databases

BioGridi4259771. 15 interactors.
DIPiDIP-11221N.
IntActiQ47149. 4 interactors.
MINTiMINT-1263057.
STRINGi316385.ECDH10B_0207.

Structurei

Secondary structure

192
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 9Combined sources5
Helixi10 – 21Combined sources12
Helixi26 – 37Combined sources12
Helixi45 – 47Combined sources3
Beta strandi53 – 55Combined sources3
Beta strandi59 – 65Combined sources7
Beta strandi68 – 74Combined sources7
Beta strandi76 – 85Combined sources10
Helixi87 – 91Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4Q2UX-ray1.80B/D/F/H/J/L/N/P2-92[»]
ProteinModelPortaliQ47149.
SMRiQ47149.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RelE toxin family. YafQ subfamily.Curated

Phylogenomic databases

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

Family and domain databases

InterProiView protein in InterPro
IPR035095. RelE-like_dom.
IPR007712. RelE/ParE_toxin.
IPR004386. Toxin_YafQ-like.
PfamiView protein in Pfam
PF15738. YafQ_toxin. 1 hit.
PIRSFiPIRSF006156. YafQ. 1 hit.
SUPFAMiSSF143011. SSF143011. 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.
PATRICifig|1411691.4.peg.2058.

Similar proteinsi

Entry informationi

Entry nameiYAFQ_ECOLI
AccessioniPrimary (citable) accession number: Q47149
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: August 30, 2017
This is version 127 of the entry and version 1 of the sequence. See 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
  3. SIMILARITY comments
    Index of protein domains and families