YEFM_ECOLI
ID YEFM_ECOLI Reviewed; 83 AA.
AC P69346; P46147; P76371;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Antitoxin YefM;
GN Name=yefM; OrderedLocusNames=b2017, JW5835;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PRELIMINARY PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6170941; DOI=10.1093/nar/9.9.2075;
RA Verde P., Frunzio R., di Nocera P.P., Blasi F., Bruni C.B.;
RT "Identification, nucleotide sequence and expression of the regulatory
RT region of the histidine operon of Escherichia coli K-12.";
RL Nucleic Acids Res. 9:2075-2086(1981).
RN [5]
RP IDENTIFICATION.
RX PubMed=7567469; DOI=10.1093/nar/23.17.3554;
RA Borodovsky M., McIninch J., Koonin E.V., Rudd K.E., Medigue C., Danchin A.;
RT "Detection of new genes in a bacterial genome using Markov models for three
RT gene classes.";
RL Nucleic Acids Res. 23:3554-3562(1995).
RN [6]
RP FUNCTION.
RX PubMed=14672926; DOI=10.1074/jbc.m308263200;
RA Cherny I., Gazit E.;
RT "The YefM antitoxin defines a family of natively unfolded proteins:
RT implications as a novel antibacterial target.";
RL J. Biol. Chem. 279:8252-8261(2004).
RN [7]
RP FUNCTION AS AN ANTITOXIN, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15009896; DOI=10.1046/j.1365-2958.2003.03941.x;
RA Christensen S.K., Maenhaut-Michel G., Mine N., Gottesman S., Gerdes K.,
RA Van Melderen L.;
RT "Overproduction of the Lon protease triggers inhibition of translation in
RT Escherichia coli: involvement of the yefM-yoeB toxin-antitoxin system.";
RL Mol. Microbiol. 51:1705-1717(2004).
RN [8]
RP SUBUNIT.
RC STRAIN=K12 / MC1061 / ATCC 53338 / DSM 7140;
RX PubMed=15980067; DOI=10.1074/jbc.m506220200;
RA Cherny I., Rockah L., Gazit E.;
RT "The YoeB toxin is a folded protein that forms a physical complex with the
RT unfolded YefM antitoxin. Implications for a structural-based differential
RT stability of toxin-antitoxin systems.";
RL J. Biol. Chem. 280:30063-30072(2005).
RN [9]
RP INDUCTION IN PERSISTER CELLS.
RC STRAIN=K12;
RX PubMed=16768798; DOI=10.1186/1471-2180-6-53;
RA Shah D., Zhang Z., Khodursky A., Kaldalu N., Kurg K., Lewis K.;
RT "Persisters: a distinct physiological state of E. coli.";
RL BMC Microbiol. 6:53-53(2006).
RN [10]
RP FUNCTION AS A TRANSCRIPTIONAL REPRESSOR, DNA-BINDING, SUBUNIT, AND
RP INDUCTION.
RX PubMed=17170003; DOI=10.1093/nar/gkl1028;
RA Kedzierska B., Lian L.Y., Hayes F.;
RT "Toxin-antitoxin regulation: bimodal interaction of YefM-YoeB with paired
RT DNA palindromes exerts transcriptional autorepression.";
RL Nucleic Acids Res. 35:325-339(2007).
RN [11]
RP FUNCTION AS A TRANSCRIPTIONAL REPRESSOR, DNA-BINDING, AND MUTAGENESIS OF
RP ARG-10 AND ARG-31.
RX PubMed=19028895; DOI=10.1128/jb.01331-08;
RA Bailey S.E., Hayes F.;
RT "Influence of operator site geometry on transcriptional control by the
RT YefM-YoeB toxin-antitoxin complex.";
RL J. Bacteriol. 191:762-772(2009).
RN [12]
RP INDUCTION BY VAPC.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=19400780; DOI=10.1111/j.1365-2958.2009.06694.x;
RA Winther K.S., Gerdes K.;
RT "Ectopic production of VapCs from Enterobacteria inhibits translation and
RT trans-activates YoeB mRNA interferase.";
RL Mol. Microbiol. 72:918-930(2009).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH YOEB, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=16109374; DOI=10.1016/j.molcel.2005.07.004;
RA Kamada K., Hanaoka F.;
RT "Conformational change in the catalytic site of the ribonuclease YoeB toxin
RT by YefM antitoxin.";
RL Mol. Cell 19:497-509(2005).
CC -!- FUNCTION: Antitoxin component of a type II toxin-antitoxin (TA) system.
CC Antitoxin that counteracts the effect of the YoeB toxin. YefM binds to
CC the promoter region of the yefM-yeoB operon to repress transcription,
CC YeoB acts as a corepressor. {ECO:0000269|PubMed:14672926,
CC ECO:0000269|PubMed:15009896, ECO:0000269|PubMed:17170003,
CC ECO:0000269|PubMed:19028895}.
CC -!- SUBUNIT: In solution exists as both a monomer and a dimer; the
CC monomeric state is more predominant. It has been described as being a
CC YefM-YeoB(2) heterotrimer (PubMed:15980067) and as a YefM(2)-YoeB
CC heterotrimer (PubMed:16109374 and PubMed:17170003). When complexed with
CC YoeB inhibits the toxin activity. {ECO:0000269|PubMed:15980067,
CC ECO:0000269|PubMed:16109374, ECO:0000269|PubMed:17170003}.
CC -!- INDUCTION: Represses its own promoter; more strongly repressed by the
CC YefM(2)YoeB heterotrimer. Induced in persister cells. Ectopic
CC expression of Salmonella or Shigella toxin VapC induces the yefM-yoeB
CC operon and also induces Yoeb toxin activity in a Lon protease-dependent
CC manner. {ECO:0000269|PubMed:16768798, ECO:0000269|PubMed:17170003,
CC ECO:0000269|PubMed:19400780}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under standard growth
CC conditions. Delays Lon protease-dependent lethality upon overexpression
CC of Lon, but does not fully suppress it. {ECO:0000269|PubMed:15009896}.
CC -!- MISCELLANEOUS: Has been described as natively unfolded and
CC proteolytically unstable in vivo (PubMed:14672926), but also as
CC structured following overexpression in vitro (PubMed:17170003). Has a
CC half-life of approximately 1 hour in vivo.
CC {ECO:0000305|PubMed:14672926, ECO:0000305|PubMed:17170003}.
CC -!- SIMILARITY: Belongs to the phD/YefM antitoxin family. {ECO:0000305}.
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DR EMBL; U00096; AAC75078.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA15849.2; -; Genomic_DNA.
DR EMBL; V00284; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; H64966; H64966.
DR RefSeq; NP_416521.2; NC_000913.3.
DR RefSeq; WP_001259255.1; NZ_STEB01000048.1.
DR PDB; 2A6Q; X-ray; 2.05 A; A/B/C/D=1-83.
DR PDBsum; 2A6Q; -.
DR AlphaFoldDB; P69346; -.
DR SMR; P69346; -.
DR BioGRID; 4263534; 149.
DR BioGRID; 850889; 1.
DR ComplexPortal; CPX-1087; YoeB-YefM toxin-antitoxin complex.
DR IntAct; P69346; 1.
DR MINT; P69346; -.
DR STRING; 511145.b2017; -.
DR ChEMBL; CHEMBL3309007; -.
DR PaxDb; P69346; -.
DR PRIDE; P69346; -.
DR EnsemblBacteria; AAC75078; AAC75078; b2017.
DR EnsemblBacteria; BAA15849; BAA15849; BAA15849.
DR GeneID; 66674085; -.
DR GeneID; 946542; -.
DR KEGG; ecj:JW5835; -.
DR KEGG; eco:b2017; -.
DR PATRIC; fig|1411691.4.peg.234; -.
DR EchoBASE; EB2693; -.
DR eggNOG; COG2161; Bacteria.
DR HOGENOM; CLU_155837_1_0_6; -.
DR InParanoid; P69346; -.
DR OMA; MRIVSFT; -.
DR PhylomeDB; P69346; -.
DR BioCyc; EcoCyc:EG12844-MON; -.
DR BioCyc; MetaCyc:EG12844-MON; -.
DR EvolutionaryTrace; P69346; -.
DR PRO; PR:P69346; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0110001; C:toxin-antitoxin complex; IPI:ComplexPortal.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:UniProtKB.
DR GO; GO:0015643; F:toxic substance binding; IDA:UniProtKB.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0040008; P:regulation of growth; IC:ComplexPortal.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IC:ComplexPortal.
DR GO; GO:0044010; P:single-species biofilm formation; IMP:EcoCyc.
DR DisProt; DP01488; -.
DR InterPro; IPR006442; Antitoxin_Phd/YefM.
DR InterPro; IPR036165; YefM-like_sf.
DR Pfam; PF02604; PhdYeFM_antitox; 1.
DR SUPFAM; SSF143120; SSF143120; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Reference proteome; Repressor;
KW Toxin-antitoxin system; Transcription; Transcription regulation.
FT CHAIN 1..83
FT /note="Antitoxin YefM"
FT /id="PRO_0000213738"
FT MUTAGEN 10
FT /note="R->A: Loss of DNA-binding and transcriptional
FT repression."
FT /evidence="ECO:0000269|PubMed:19028895"
FT MUTAGEN 31
FT /note="R->A: Loss of DNA-binding and transcriptional
FT repression."
FT /evidence="ECO:0000269|PubMed:19028895"
FT STRAND 1..5
FT /evidence="ECO:0007829|PDB:2A6Q"
FT HELIX 6..11
FT /evidence="ECO:0007829|PDB:2A6Q"
FT HELIX 13..23
FT /evidence="ECO:0007829|PDB:2A6Q"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:2A6Q"
FT STRAND 36..41
FT /evidence="ECO:0007829|PDB:2A6Q"
FT HELIX 42..56
FT /evidence="ECO:0007829|PDB:2A6Q"
FT HELIX 58..72
FT /evidence="ECO:0007829|PDB:2A6Q"
SQ SEQUENCE 83 AA; 9308 MW; 6D5C9A49DC8D8E8E CRC64;
MRTISYSEAR QNLSATMMKA VEDHAPILIT RQNGEACVLM SLEEYNSLEE TAYLLRSPAN
ARRLMDSIDS LKSGKGTEKD IIE
