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Protein

Antitoxin YefM

Gene

yefM

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Antitoxin component of a toxin-antitoxin (TA) module. 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

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
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12844-MONOMER.
ECOL316407:JW5835-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi10 – 101R → A: Loss of DNA-binding and transcriptional repression. 1 Publication
Mutagenesisi31 – 311R → A: Loss of DNA-binding and transcriptional repression. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8383Antitoxin YefMPRO_0000213738Add
BLAST

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 YefM(2)-YoeB heterotrimer (PubMed:16109374 and PubMed:17170003). When complexed with YoeB inhibits the toxin activity.3 Publications

Protein-protein interaction databases

BioGridi4263534. 149 interactions.
IntActiP69346. 1 interaction.
STRINGi511145.b2017.

Structurei

Secondary structure

83
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 55Combined sources
Helixi6 – 116Combined sources
Helixi13 – 2311Combined sources
Beta strandi27 – 304Combined sources
Beta strandi36 – 416Combined sources
Helixi42 – 5615Combined sources
Helixi58 – 7215Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2A6QX-ray2.05A/B/C/D1-83[»]
ProteinModelPortaliP69346.
SMRiP69346. Positions 1-83.
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.
OMAiQETAYLM.
OrthoDBiEOG651T2N.
PhylomeDBiP69346.

Family and domain databases

Gene3Di3.40.1620.10. 1 hit.
InterProiIPR006442. Antitoxin_Phd/YefM.
[Graphical view]
PfamiPF02604. PhdYeFM_antitox. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01552. phd_fam. 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.
PATRICi32119371. VBIEscCol129921_2095.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2A6QX-ray2.05A/B/C/D1-83[»]
ProteinModelPortaliP69346.
SMRiP69346. Positions 1-83.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263534. 149 interactions.
IntActiP69346. 1 interaction.
STRINGi511145.b2017.

Proteomic databases

PaxDbiP69346.
PRIDEiP69346.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75078; AAC75078; b2017.
BAA15849; BAA15849; BAA15849.
GeneIDi946542.
KEGGiecj:JW5835.
eco:b2017.
PATRICi32119371. VBIEscCol129921_2095.

Organism-specific databases

EchoBASEiEB2693.
EcoGeneiEG12844. yefM.

Phylogenomic databases

eggNOGiENOG4105VTW. Bacteria.
COG2161. LUCA.
HOGENOMiHOG000216358.
InParanoidiP69346.
KOiK19159.
OMAiQETAYLM.
OrthoDBiEOG651T2N.
PhylomeDBiP69346.

Enzyme and pathway databases

BioCyciEcoCyc:EG12844-MONOMER.
ECOL316407:JW5835-MONOMER.
MetaCyc:EG12844-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP69346.
PROiP69346.

Family and domain databases

Gene3Di3.40.1620.10. 1 hit.
InterProiIPR006442. Antitoxin_Phd/YefM.
[Graphical view]
PfamiPF02604. PhdYeFM_antitox. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01552. phd_fam. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Identification, nucleotide sequence and expression of the regulatory region of the histidine operon of Escherichia coli K-12."
    Verde P., Frunzio R., di Nocera P.P., Blasi F., Bruni C.B.
    Nucleic Acids Res. 9:2075-2086(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  5. "Detection of new genes in a bacterial genome using Markov models for three gene classes."
    Borodovsky M., McIninch J., Koonin E.V., Rudd K.E., Medigue C., Danchin A.
    Nucleic Acids Res. 23:3554-3562(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  6. "The YefM antitoxin defines a family of natively unfolded proteins: implications as a novel antibacterial target."
    Cherny I., Gazit E.
    J. Biol. Chem. 279:8252-8261(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Overproduction of the Lon protease triggers inhibition of translation in Escherichia coli: involvement of the yefM-yoeB toxin-antitoxin system."
    Christensen S.K., Maenhaut-Michel G., Mine N., Gottesman S., Gerdes K., Van Melderen L.
    Mol. Microbiol. 51:1705-1717(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN ANTITOXIN, DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / ATCC 47076.
  8. "The YoeB toxin is a folded protein that forms a physical complex with the unfolded YefM antitoxin. Implications for a structural-based differential stability of toxin-antitoxin systems."
    Cherny I., Rockah L., Gazit E.
    J. Biol. Chem. 280:30063-30072(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
    Strain: K12 / MC1061 / ATCC 53338 / DSM 7140.
  9. "Persisters: a distinct physiological state of E. coli."
    Shah D., Zhang Z., Khodursky A., Kaldalu N., Kurg K., Lewis K.
    BMC Microbiol. 6:53-53(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION IN PERSISTER CELLS.
    Strain: K12.
  10. "Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression."
    Kedzierska B., Lian L.Y., Hayes F.
    Nucleic Acids Res. 35:325-339(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TRANSCRIPTIONAL REPRESSOR, DNA-BINDING, SUBUNIT, INDUCTION.
  11. "Influence of operator site geometry on transcriptional control by the YefM-YoeB toxin-antitoxin complex."
    Bailey S.E., Hayes F.
    J. Bacteriol. 191:762-772(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TRANSCRIPTIONAL REPRESSOR, DNA-BINDING, MUTAGENESIS OF ARG-10 AND ARG-31.
  12. "Ectopic production of VapCs from Enterobacteria inhibits translation and trans-activates YoeB mRNA interferase."
    Winther K.S., Gerdes K.
    Mol. Microbiol. 72:918-930(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY VAPC.
    Strain: K12 / MG1655 / ATCC 47076.
  13. "Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin."
    Kamada K., Hanaoka F.
    Mol. Cell 19:497-509(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH YOEB, SUBUNIT.
    Strain: K12.

Entry informationi

Entry nameiYEFM_ECOLI
AccessioniPrimary (citable) accession number: P69346
Secondary accession number(s): P46147, P76371
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2005
Last modified: April 13, 2016
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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

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.