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Protein

Toxin YoeB

Gene

yoeB

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

Functioni

Toxic component of a toxin-antitoxin (TA) module. Its mode of function is controversial; it has been proposed to be an mRNA interferase but also an inhibitor of translation initiation. When overproduced in wild-type cells, inhibits bacterial growth and translation by cleavage of mRNA molecules while it has a weak effect on colony forming ability. Overproduction of Lon protease specifically activates YoeB-dependent mRNA cleavage, leading to lethality. YefM binds to the promoter region of the yefM-yeoB operon to repress transcription, YeoB acts as a corepressor.
Shown in vitro to be an mRNA interferase that requires translation for substrate cleavage; if the mRNA is mutated so as to not be translatable it is no longer cleaved. Cleavage only occurs within translated regions. Has RNase activity and preferentially cleaves at the 3'-end of purine ribonucleotides.
Also shown in vitro to be a translation initiation blocker. Binds to the 70S ribosome and 50S ribosomal subunit; binding is inhibited by hygromycin A and tetracycline, both of which bind to the 30S subunit in the A site. Thus YoeB is located at the interface between 50S and 30S ribosomes and interacts with the A site where it cleaves mRNA, blocking translation initiation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei46 – 461Proton acceptor1 Publication
Active sitei83 – 831Proton donor1 Publication

GO - Molecular functioni

  • endoribonuclease activity Source: EcoCyc
  • endoribonuclease activity, producing 3'-phosphomonoesters Source: EcoCyc
  • ribosomal small subunit binding Source: EcoCyc
  • RNA binding Source: UniProtKB-KW
  • transcription corepressor activity Source: UniProtKB

GO - Biological processi

  • mRNA catabolic process Source: EcoCyc
  • mRNA cleavage involved in gene silencing Source: UniProtKB
  • negative regulation of translational initiation Source: EcoCyc
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • single-species biofilm formation Source: EcoCyc
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Repressor, Toxin

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:MONOMER0-1041.
ECOL316407:JW5331-MONOMER.
MetaCyc:MONOMER0-1041.

Names & Taxonomyi

Protein namesi
Recommended name:
Toxin YoeB (EC:3.1.-.-)
Alternative name(s):
Putative endoribonuclease YoeB
Putative mRNA interferase Yoeb
Gene namesi
Name:yoeB
Ordered Locus Names:b4539, JW5331
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14356. yoeB.

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. No loss of ability to form persister cells.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi65 – 651R → A: Loss of RNase activity. 1 Publication
Mutagenesisi83 – 831H → Q: Loss of RNase activity; still see mRNA cleavage in association with 70S ribosomes. 2 Publications
Mutagenesisi84 – 841Y → A: Loss of RNase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8484Toxin YoeBPRO_0000216209Add
BLAST

Proteomic databases

PaxDbiP69348.

Expressioni

Inductioni

Repressed by YefM, 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

Forms a complex with antitoxin YefM, in which the toxin is inactive. It has been described as being a YefM-YeoB2 heterotrimer (PubMed:15980067). Also described as a YefM(2)-YoeB heterotrimer (PubMed:16109374 and PubMed:17170003). Binds the 50S ribosomal subunit.3 Publications

Protein-protein interaction databases

BioGridi4260402. 128 interactions.
IntActiP69348. 1 interaction.
STRINGi511145.b4539.

Structurei

Secondary structure

1
84
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54Combined sources
Helixi7 – 1711Combined sources
Helixi21 – 3616Combined sources
Helixi50 – 523Combined sources
Beta strandi56 – 638Combined sources
Beta strandi65 – 706Combined sources
Beta strandi72 – 8110Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2A6QX-ray2.05E/F1-84[»]
2A6RX-ray2.05A/B/C/D/E/F1-84[»]
2A6SX-ray1.77A/B/C/D1-84[»]
4V8XX-ray3.35AY/AZ/CY/CZ1-84[»]
ProteinModelPortaliP69348.
SMRiP69348. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69348.

Family & Domainsi

Sequence similaritiesi

Belongs to the YoeB family.Curated

Phylogenomic databases

eggNOGiENOG4105KRQ. Bacteria.
COG4115. LUCA.
HOGENOMiHOG000216470.
InParanoidiP69348.
KOiK19158.
OMAiKCRFHYD.
OrthoDBiEOG6KWZ5K.
PhylomeDBiP69348.

Family and domain databases

InterProiIPR009614. YoeB_toxin.
[Graphical view]
PfamiPF06769. YoeB_toxin. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02116. toxin_Txe_YoeB. 1 hit.

Sequencei

Sequence statusi: Complete.

P69348-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLIWSEESW DDYLYWQETD KRIVKKINEL IKDTRRTPFE GKGKPEPLKH
60 70 80
NLSGFWSRRI TEEHRLVYAV TDDSLLIAAC RYHY
Length:84
Mass (Da):10,216
Last modified:March 1, 2005 - v1
Checksum:iC043381C56DC2939
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: ABD18681.1.
AP009048 Genomic DNA. Translation: BAE76569.1.
RefSeqiWP_000767829.1. NZ_LN832404.1.
YP_588458.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiABD18681; ABD18681; b4539.
BAE76569; BAE76569; BAE76569.
GeneIDi1450274.
KEGGiecj:JW5331.
eco:b4539.
PATRICi32119369. VBIEscCol129921_2094.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: ABD18681.1.
AP009048 Genomic DNA. Translation: BAE76569.1.
RefSeqiWP_000767829.1. NZ_LN832404.1.
YP_588458.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2A6QX-ray2.05E/F1-84[»]
2A6RX-ray2.05A/B/C/D/E/F1-84[»]
2A6SX-ray1.77A/B/C/D1-84[»]
4V8XX-ray3.35AY/AZ/CY/CZ1-84[»]
ProteinModelPortaliP69348.
SMRiP69348. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260402. 128 interactions.
IntActiP69348. 1 interaction.
STRINGi511145.b4539.

Proteomic databases

PaxDbiP69348.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD18681; ABD18681; b4539.
BAE76569; BAE76569; BAE76569.
GeneIDi1450274.
KEGGiecj:JW5331.
eco:b4539.
PATRICi32119369. VBIEscCol129921_2094.

Organism-specific databases

EchoBASEiEB4102.
EcoGeneiEG14356. yoeB.

Phylogenomic databases

eggNOGiENOG4105KRQ. Bacteria.
COG4115. LUCA.
HOGENOMiHOG000216470.
InParanoidiP69348.
KOiK19158.
OMAiKCRFHYD.
OrthoDBiEOG6KWZ5K.
PhylomeDBiP69348.

Enzyme and pathway databases

BioCyciEcoCyc:MONOMER0-1041.
ECOL316407:JW5331-MONOMER.
MetaCyc:MONOMER0-1041.

Miscellaneous databases

EvolutionaryTraceiP69348.
PROiP69348.

Family and domain databases

InterProiIPR009614. YoeB_toxin.
[Graphical view]
PfamiPF06769. YoeB_toxin. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02116. toxin_Txe_YoeB. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "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.
  3. "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.
  4. "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 ENDORIBONUCLEASE, DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / ATCC 47076.
  5. "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.
  6. "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, DISRUPTION PHENOTYPE.
    Strain: K12.
  7. "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 COREPRESSOR, SUBUNIT, INDUCTION.
  8. "Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms."
    Christensen-Dalsgaard M., Gerdes K.
    Nucleic Acids Res. 36:6472-6481(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Strain: K12.
  9. "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 COREPRESSOR.
  10. "The inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli toxin."
    Zhang Y., Inouye M.
    J. Biol. Chem. 284:6627-6638(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TRANSLATION INITIATION BLOCKER, RIBOSOME-BINDING, MUTAGENESIS OF HIS-83.
  11. "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: FUNCTION AS A TOXIN, INDUCTION BY VAPC.
    Strain: K12 / MG1655 / ATCC 47076.
  12. "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 YEFM, FUNCTION AS A RIBONUCLEASE, SUBUNIT, ACTIVE SITES, MUTAGENESIS OF ARG-65; HIS-83 AND TYR-84.
    Strain: K12.

Entry informationi

Entry nameiYOEB_ECOLI
AccessioniPrimary (citable) accession number: P69348
Secondary accession number(s): P56605, Q2EES4, Q2MAY7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2005
Last modified: July 6, 2016
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.