RegulonDB RegulonDB 11.1: Gene Form
   

yoeB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yeeZ yoeB yefM hisL YefM-YoeB YefM YefM-YoeB YefM DksA-ppGpp DksA-ppGpp Cis-reg; leader TSS_2331 (cluster) TSS_2331 (cluster) TSS_2330 (cluster) TSS_2330 (cluster) TSS_2329 TSS_2329 hisLp hisLp TSS_2327 TSS_2327 yefMp yefMp TSS_2325 TSS_2325 yeeZp5 yeeZp5 yeeZp7 yeeZp7 TSS_2324 TSS_2324 TSS_2323 TSS_2323

Gene      
Name: yoeB    Texpresso search in the literature
Synonym(s): ECK2011, G0-9121, b4539
Genome position(nucleotides): 2089211 <-- 2089465
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 44.31
External database links:  
ASAP:
 ABE-0285060
ECHOBASE:
 EB4102
ECOLIHUB:
 yoeB
STRING:
 511145.b4539
COLOMBOS: yoeB


Product      
Name: ribosome-dependent mRNA interferase toxin YoeB
Synonym(s): YoeB, toxin of the YoeB-YefM toxin-antitoxin pair
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 10.216
Isoelectric point: 8.448
Motif(s):
 
Type Positions Sequence Comment
5 -> 84 WSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY
65 -> 65 R UniProt: Loss of RNase activity..
83 -> 83 H UniProt: Loss of RNase activity; still see mRNA cleavage in association with 70S ribosomes..
84 -> 84 Y UniProt: Loss of RNase activity..

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.10 - defense/survival
Gene Ontology Terms (GO)  
cellular_component GO:0110001 - toxin-antitoxin complex
GO:0005829 - cytosol
molecular_function GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0003723 - RNA binding
GO:0004521 - endoribonuclease activity
GO:0016892 - endoribonuclease activity, producing 3'-phosphomonoesters
GO:0042803 - protein homodimerization activity
GO:0043024 - ribosomal small subunit binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006401 - RNA catabolic process
GO:0009408 - response to heat
GO:0045947 - negative regulation of translational initiation
GO:0006402 - mRNA catabolic process
GO:0040008 - regulation of growth
GO:0044010 - single-species biofilm formation
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic
GO:1903507 - negative regulation of nucleic acid-templated transcription
GO:0098795 - mRNA destabilization-mediated gene silencing
External database links:  
ALPHAFOLD:
 P69348
ECOCYC:
 MONOMER0-1041
ECOLIWIKI:
 b4539
INTERPRO:
 IPR009614
INTERPRO:
 IPR035093
MINT:
 P69348
PANTHER:
 PTHR38039
PDB:
 6NY6
PDB:
 2A6R
PDB:
 2A6S
PDB:
 4V8X
PDB:
 2A6Q
PFAM:
 PF06769
PRIDE:
 P69348
REFSEQ:
 YP_588458
SMR:
 P69348
UNIPROT:
 P69348


Operon      
Name: yefM-yoeB         
Operon arrangement:
Transcription unit        Promoter
yefM-yoeB


Transcriptional Regulation      
Display Regulation             
Repressed by: YefM-YoeB, YefM


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_2323 2089152 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2324 2089158 reverse nd [RS-EPT-CBR] [1]
  promoter yeeZp7 2089176 reverse nd [COMP-AINF] [2]
  promoter yeeZp5 2089211 reverse nd [COMP-AINF] [2]
  promoter TSS_2325 2089731 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2327 2089902 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2329 2089980 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2330 (cluster) 2089990 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2331 (cluster) 2089999 forward nd [RS-EPT-CBR] [1]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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