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Protein

mRNA interferase toxin YafQ

Gene

yafQ

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

Functioni

Toxic component of a type II toxin-antitoxin (TA) system (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 systems 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
Biological processToxin-antitoxin system, Transcription, 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
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
OMAiENYQDHA
PhylomeDBiQ47149

Family and domain databases

Gene3Di3.30.2310.20, 1 hit
InterProiView protein in InterPro
IPR007712 RelE/ParE_toxin
IPR035093 RelE/ParE_toxin_dom_sf
IPR004386 Toxin_YafQ-like
PANTHERiPTHR40588 PTHR40588, 1 hit
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

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: March 28, 2018
This is version 132 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
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health