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Protein

Antitoxin YefM

Gene

yefM

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

Functioni

Antitoxin component of a type II toxin-antitoxin (TA) system. Antitoxin that counteracts the effect of the YoeB toxin. YefM binds to the promoter region of the yefM-yeoB operon to repress transcription, YeoB acts as a corepressor.4 Publications

Miscellaneous

Has been described as natively unfolded and proteolytically unstable in vivo (PubMed:14672926), but also as structured following overexpression in vitro (PubMed:17170003). Has a half-life of approximately 1 hour in vivo.2 Publications

GO - Molecular functioni

  • sequence-specific DNA binding Source: UniProtKB
  • toxic substance binding Source: UniProtKB

GO - Biological processi

  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • single-species biofilm formation Source: EcoCyc
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processToxin-antitoxin system, Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciEcoCyc:EG12844-MONOMER
MetaCyc:EG12844-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Antitoxin YefM
Gene namesi
Name:yefM
Ordered Locus Names:b2017, JW5835
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12844 yefM

Pathology & Biotechi

Disruption phenotypei

No visible phenotype under standard growth conditions. Delays Lon protease-dependent lethality upon overexpression of Lon, but does not fully suppress it.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi10R → A: Loss of DNA-binding and transcriptional repression. 1 Publication1
Mutagenesisi31R → A: Loss of DNA-binding and transcriptional repression. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002137381 – 83Antitoxin YefMAdd BLAST83

Proteomic databases

PaxDbiP69346
PRIDEiP69346

Expressioni

Inductioni

Represses its own promoter; more strongly repressed by the YefM2YoeB heterotrimer. Induced in persister cells. Ectopic expression of Salmonella or Shigella toxin VapC induces the yefM-yoeB operon and also induces Yoeb toxin activity in a Lon protease-dependent manner.3 Publications

Interactioni

Subunit structurei

In solution exists as both a monomer and a dimer; the monomeric state is more predominant. It has been described as being a YefM-YeoB2 heterotrimer (PubMed:15980067) and as a YefM2-YoeB heterotrimer (PubMed:16109374 and PubMed:17170003). When complexed with YoeB inhibits the toxin activity.3 Publications

Protein-protein interaction databases

BioGridi4263534, 149 interactors
IntActiP69346, 1 interactor
MINTiP69346
STRINGi316385.ECDH10B_2165

Structurei

Secondary structure

183
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 5Combined sources5
Helixi6 – 11Combined sources6
Helixi13 – 23Combined sources11
Beta strandi27 – 30Combined sources4
Beta strandi36 – 41Combined sources6
Helixi42 – 56Combined sources15
Helixi58 – 72Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2A6QX-ray2.05A/B/C/D1-83[»]
ProteinModelPortaliP69346
SMRiP69346
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69346

Family & Domainsi

Sequence similaritiesi

Belongs to the phD/YefM antitoxin family.Curated

Phylogenomic databases

eggNOGiENOG4105VTW Bacteria
COG2161 LUCA
HOGENOMiHOG000216358
InParanoidiP69346
KOiK19159
OMAiMRIVSFT
PhylomeDBiP69346

Family and domain databases

InterProiView protein in InterPro
IPR006442 Antitoxin_Phd/YefM
IPR036165 YefM-like_sf
PfamiView protein in Pfam
PF02604 PhdYeFM_antitox, 1 hit
SUPFAMiSSF143120 SSF143120, 1 hit

Sequencei

Sequence statusi: Complete.

P69346-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRTISYSEAR QNLSATMMKA VEDHAPILIT RQNGEACVLM SLEEYNSLEE
60 70 80
TAYLLRSPAN ARRLMDSIDS LKSGKGTEKD IIE
Length:83
Mass (Da):9,308
Last modified:March 1, 2005 - v1
Checksum:i6D5C9A49DC8D8E8E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC75078.2
AP009048 Genomic DNA Translation: BAA15849.2
V00284 Genomic DNA No translation available.
PIRiH64966
RefSeqiNP_416521.2, NC_000913.3
WP_001259255.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75078; AAC75078; b2017
BAA15849; BAA15849; BAA15849
GeneIDi946542
KEGGiecj:JW5835
eco:b2017
PATRICifig|1411691.4.peg.234

Similar proteinsi

Entry informationi

Entry nameiYEFM_ECOLI
AccessioniPrimary (citable) accession number: P69346
Secondary accession number(s): P46147, P76371
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2005
Last modified: March 28, 2018
This is version 94 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
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Main funding by: National Institutes of Health