YOEB_ECOLI
ID YOEB_ECOLI Reviewed; 84 AA.
AC P69348; P56605; Q2EES4; Q2MAY7;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Toxin YoeB;
DE EC=3.1.-.-;
DE AltName: Full=Putative endoribonuclease YoeB;
DE AltName: Full=Putative mRNA interferase Yoeb;
GN Name=yoeB; OrderedLocusNames=b4539, JW5331;
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 / 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 [2]
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 [3]
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 [4]
RP FUNCTION AS AN ENDORIBONUCLEASE, 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 [5]
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 [6]
RP INDUCTION IN PERSISTER CELLS, AND DISRUPTION PHENOTYPE.
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 [7]
RP FUNCTION AS A TRANSCRIPTIONAL COREPRESSOR, SUBUNIT, AND 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 [8]
RP FUNCTION.
RC STRAIN=K12;
RX PubMed=18854355; DOI=10.1093/nar/gkn667;
RA Christensen-Dalsgaard M., Gerdes K.;
RT "Translation affects YoeB and MazF messenger RNA interferase activities by
RT different mechanisms.";
RL Nucleic Acids Res. 36:6472-6481(2008).
RN [9]
RP FUNCTION AS A TRANSCRIPTIONAL COREPRESSOR.
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 [10]
RP FUNCTION AS A TRANSLATION INITIATION BLOCKER, RIBOSOME-BINDING, AND
RP MUTAGENESIS OF HIS-83.
RX PubMed=19124462; DOI=10.1074/jbc.m808779200;
RA Zhang Y., Inouye M.;
RT "The inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli
RT toxin.";
RL J. Biol. Chem. 284:6627-6638(2009).
RN [11]
RP FUNCTION AS A TOXIN, AND 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 [12]
RP RETRACTED PAPER.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21788497; DOI=10.1073/pnas.1100186108;
RA Maisonneuve E., Shakespeare L.J., Joergensen M.G., Gerdes K.;
RT "Bacterial persistence by RNA endonucleases.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:13206-13211(2011).
RN [13]
RP RETRACTION NOTICE OF PUBMED:21788497.
RX PubMed=29531044; DOI=10.1073/pnas.1803278115;
RA Maisonneuve E., Shakespeare L.J., Joergensen M.G., Gerdes K.;
RL Proc. Natl. Acad. Sci. U.S.A. 115:E2901-E2901(2018).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH YEFM, FUNCTION AS A
RP RIBONUCLEASE, SUBUNIT, ACTIVE SITES, AND MUTAGENESIS OF ARG-65; HIS-83 AND
RP TYR-84.
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: Toxic component of a type II toxin-antitoxin (TA) system. Its
CC mode of function is controversial; it has been proposed to be an mRNA
CC interferase but also an inhibitor of translation initiation. When
CC overproduced in wild-type cells, inhibits bacterial growth and
CC translation by cleavage of mRNA molecules while it has a weak effect on
CC colony forming ability. Overproduction of Lon protease specifically
CC activates YoeB-dependent mRNA cleavage, leading to lethality. YefM
CC binds to the promoter region of the yefM-yeoB operon to repress
CC transcription, YeoB acts as a corepressor.
CC -!- FUNCTION: Shown in vitro to be an mRNA interferase that requires
CC translation for substrate cleavage; if the mRNA is mutated so as to not
CC be translatable it is no longer cleaved. Cleavage only occurs within
CC translated regions. Has RNase activity and preferentially cleaves at
CC the 3'-end of purine ribonucleotides. {ECO:0000269|PubMed:16109374}.
CC -!- FUNCTION: Also shown in vitro to be a translation initiation blocker.
CC Binds to the 70S ribosome and 50S ribosomal subunit; binding is
CC inhibited by hygromycin A and tetracycline, both of which bind to the
CC 30S subunit in the A site. Thus YoeB is located at the interface
CC between 50S and 30S ribosomes and interacts with the A site where it
CC cleaves mRNA, blocking translation initiation.
CC -!- SUBUNIT: Forms a complex with antitoxin YefM, in which the toxin is
CC inactive. It has been described as being a YefM-YeoB(2) heterotrimer
CC (PubMed:15980067). Also described as a YefM(2)-YoeB heterotrimer
CC (PubMed:16109374 and PubMed:17170003). Binds the 50S ribosomal subunit.
CC {ECO:0000269|PubMed:15980067, ECO:0000269|PubMed:16109374,
CC ECO:0000269|PubMed:17170003}.
CC -!- INDUCTION: Repressed by YefM, 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. No loss of ability to form
CC persister cells. {ECO:0000269|PubMed:15009896,
CC ECO:0000269|PubMed:16768798}.
CC -!- SIMILARITY: Belongs to the YoeB family. {ECO:0000305}.
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DR EMBL; U00096; ABD18681.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76569.1; -; Genomic_DNA.
DR RefSeq; WP_000767829.1; NZ_STEB01000048.1.
DR RefSeq; YP_588458.1; NC_000913.3.
DR PDB; 2A6Q; X-ray; 2.05 A; E/F=1-84.
DR PDB; 2A6R; X-ray; 2.05 A; A/B/C/D/E/F=1-84.
DR PDB; 2A6S; X-ray; 1.77 A; A/B/C/D=1-84.
DR PDB; 4V8X; X-ray; 3.35 A; AY/AZ/CY/CZ=1-84.
DR PDB; 6NY6; X-ray; 3.74 A; Y/Z=1-84.
DR PDBsum; 2A6Q; -.
DR PDBsum; 2A6R; -.
DR PDBsum; 2A6S; -.
DR PDBsum; 4V8X; -.
DR PDBsum; 6NY6; -.
DR AlphaFoldDB; P69348; -.
DR SMR; P69348; -.
DR BioGRID; 4260402; 128.
DR BioGRID; 853399; 1.
DR ComplexPortal; CPX-1087; YoeB-YefM toxin-antitoxin complex.
DR IntAct; P69348; 1.
DR MINT; P69348; -.
DR STRING; 511145.b4539; -.
DR PaxDb; P69348; -.
DR PRIDE; P69348; -.
DR EnsemblBacteria; ABD18681; ABD18681; b4539.
DR EnsemblBacteria; BAE76569; BAE76569; BAE76569.
DR GeneID; 1450274; -.
DR GeneID; 66674086; -.
DR KEGG; ecj:JW5331; -.
DR KEGG; eco:b4539; -.
DR PATRIC; fig|1411691.4.peg.235; -.
DR EchoBASE; EB4102; -.
DR eggNOG; COG4115; Bacteria.
DR HOGENOM; CLU_169492_2_2_6; -.
DR InParanoid; P69348; -.
DR OMA; KCRFHYD; -.
DR PhylomeDB; P69348; -.
DR BioCyc; EcoCyc:MON0-1041; -.
DR BioCyc; MetaCyc:MON0-1041; -.
DR EvolutionaryTrace; P69348; -.
DR PRO; PR:P69348; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0110001; C:toxin-antitoxin complex; IPI:ComplexPortal.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:EcoCyc.
DR GO; GO:0016892; F:endoribonuclease activity, producing 3'-phosphomonoesters; IDA:EcoCyc.
DR GO; GO:0043024; F:ribosomal small subunit binding; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0098795; P:global gene silencing by mRNA cleavage; IDA:UniProtKB.
DR GO; GO:0006402; P:mRNA catabolic process; IDA:EcoCyc.
DR GO; GO:1903507; P:negative regulation of nucleic acid-templated transcription; IBA:GO_Central.
DR GO; GO:0045947; P:negative regulation of translational initiation; IDA:EcoCyc.
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:0009408; P:response to heat; IMP:EcoCyc.
DR GO; GO:0006401; P:RNA catabolic process; IBA:GO_Central.
DR GO; GO:0044010; P:single-species biofilm formation; IMP:EcoCyc.
DR Gene3D; 3.30.2310.20; -; 1.
DR InterPro; IPR035093; RelE/ParE_toxin_dom_sf.
DR InterPro; IPR009614; YoeB_toxin.
DR PANTHER; PTHR38039; PTHR38039; 1.
DR Pfam; PF06769; YoeB_toxin; 1.
DR SUPFAM; SSF143011; SSF143011; 1.
DR TIGRFAMs; TIGR02116; toxin_Txe_YoeB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Endonuclease; Hydrolase; Nuclease; Reference proteome;
KW Repressor; RNA-binding; Toxin-antitoxin system; Transcription;
KW Transcription regulation.
FT CHAIN 1..84
FT /note="Toxin YoeB"
FT /id="PRO_0000216209"
FT ACT_SITE 46
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:16109374"
FT ACT_SITE 83
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:16109374"
FT MUTAGEN 65
FT /note="R->A: Loss of RNase activity."
FT /evidence="ECO:0000269|PubMed:16109374"
FT MUTAGEN 83
FT /note="H->Q: Loss of RNase activity; still see mRNA
FT cleavage in association with 70S ribosomes."
FT /evidence="ECO:0000269|PubMed:16109374,
FT ECO:0000269|PubMed:19124462"
FT MUTAGEN 84
FT /note="Y->A: Loss of RNase activity."
FT /evidence="ECO:0000269|PubMed:16109374"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:2A6S"
FT HELIX 7..17
FT /evidence="ECO:0007829|PDB:2A6S"
FT HELIX 21..36
FT /evidence="ECO:0007829|PDB:2A6S"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:2A6S"
FT STRAND 56..63
FT /evidence="ECO:0007829|PDB:2A6S"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:2A6S"
FT STRAND 72..81
FT /evidence="ECO:0007829|PDB:2A6S"
SQ SEQUENCE 84 AA; 10216 MW; C043381C56DC2939 CRC64;
MKLIWSEESW DDYLYWQETD KRIVKKINEL IKDTRRTPFE GKGKPEPLKH NLSGFWSRRI
TEEHRLVYAV TDDSLLIAAC RYHY
