RegulonDB RegulonDB 11.1: Gene Form
   

yafQ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dpaA yafQ dinJ yafJ TSS_444 TSS_444 yafKp6 yafKp6

Gene      
Name: yafQ    Texpresso search in the literature
Synonym(s): ECK0226, G6109, b0225
Genome position(nucleotides): 245961 <-- 246239
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 39.43
External database links:  
ASAP:
 ABE-0000761
ECHOBASE:
 EB2948
ECOLIHUB:
 yafQ
OU-MICROARRAY:
 b0225
STRING:
 511145.b0225
COLOMBOS: yafQ


Product      
Name: ribosome-dependent mRNA interferase toxin YafQ
Synonym(s): YafQ, toxin of the YafQ-DinJ toxin-antitoxin system
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 10.847
Isoelectric point: 9.999
Motif(s):
 
Type Positions Sequence Comment
5 -> 92 DIEYSGQYSKDVKLAQKRHKDMNKLKYLMTLLINNTLPLPAVYKDHPLQGSWKGYRDAHVEPDWILIYKLTDKLLRFERTGTHAALFG
87 -> 87 H UniProt: Loss of mRNA cleavage, loss of toxic effect. Still associates with the ribosome..

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection --> 5.6.3 - cell killing
Gene Ontology Terms (GO)  
cellular_component GO:0110001 - toxin-antitoxin complex
molecular_function GO:0003677 - DNA binding
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0043022 - ribosome binding
GO:0003723 - RNA binding
GO:0004521 - endoribonuclease activity
GO:0016892 - endoribonuclease activity, producing 3'-phosphomonoesters
biological_process GO:0045892 - negative regulation of transcription, DNA-templated
GO:0006402 - mRNA catabolic process
GO:0046677 - response to antibiotic
GO:0006415 - translational termination
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
Note(s): Note(s): ...[more].
Reference(s): [1] Liang Y., et al., 2014
External database links:  
ALPHAFOLD:
 Q47149
DIP:
 DIP-11221N
ECOCYC:
 G6109-MONOMER
ECOLIWIKI:
 b0225
INTERPRO:
 IPR004386
INTERPRO:
 IPR035093
INTERPRO:
 IPR007712
PANTHER:
 PTHR40588
PDB:
 4Q2U
PFAM:
 PF15738
PRIDE:
 Q47149
REFSEQ:
 NP_414760
SMR:
 Q47149
SWISSMODEL:
 Q47149
UNIPROT:
 Q47149


Operon      
Name: dinJ-yafQ         
Operon arrangement:
Transcription unit        Promoter
dinJ-yafQ


Transcriptional Regulation      
Display Regulation             
Repressed by: DinJ-YafQ, LexA


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 yafKp6 245993 reverse nd [COMP-AINF] [2]
  promoter TSS_444 246205 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Liang Y., Gao Z., Wang F., Zhang Y., Dong Y., Liu Q., 2014, Structural and functional characterization of Escherichia coli toxin-antitoxin complex DinJ-YafQ., J Biol Chem 289(30):21191-202

 [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

 [3] 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.

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