RegulonDB RegulonDB 10.10: Gene Form
   

arfB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nlpE yaeQ arfB yaeP rof CRP TSS_396 TSS_396 yaeQp yaeQp TSS_395 TSS_395 TSS_394 TSS_394 yaeQp6 yaeQp6 yaePp yaePp TSS_393 TSS_393 yaeQp3 yaeQp3

Gene      
Name: arfB    Texpresso search in the literature
Synonym(s): ECK0191, EG12354, b0191, yaeJ
Genome position(nucleotides): 214833 --> 215255 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.14
External database links:  
ASAP:
 ABE-0000650
ECHOBASE:
 EB2258
ECOLIHUB:
 yaeJ
OU-MICROARRAY:
 b0191
STRING:
 511145.b0191
COLOMBOS: arfB


Product      
Name: peptidyl-tRNA hydrolase, ribosome rescue factor
Synonym(s): ArfB, YaeJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 15.623
Isoelectric point: 11.418
Motif(s):
 
Type Positions Sequence
28 -> 28 Q
8 -> 132 VAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKARRPTRPTRASKERRLASKAQKSSVKAMR
26 -> 27 GG
27 -> 28 GQ

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003747 - translation release factor activity
GO:0016787 - hydrolase activity
GO:0043022 - ribosome binding
GO:0004045 - aminoacyl-tRNA hydrolase activity
biological_process GO:0006417 - regulation of translation
GO:0006415 - translational termination
GO:0072344 - rescue of stalled ribosome
Note(s): Note(s): ...[more].
Reference(s): [1] Kogure H., et al., 2014
[2] Ohtake K., et al., 2012
External database links:  
ECOCYC:
 EG12354-MONOMER
ECOLIWIKI:
 b0191
INTERPRO:
 IPR000352
MODBASE:
 P40711
PDB:
 2RTX
PDB:
 4V95
PFAM:
 PF00472
PRIDE:
 P40711
PROSITE:
 PS00745
REFSEQ:
 NP_414733
SMR:
 P40711
UNIPROT:
 P40711


Operon      
Name: yaeQ-arfB-nlpE         
Operon arrangement:
Transcription unit        Promoter
yaeQ-arfB-nlpE


Transcriptional Regulation      
Display Regulation             
Repressed by: CRP


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 yaeQp3 214088 forward nd [ICWHO] [3]
  promoter TSS_393 214163 reverse nd [RS-EPT-CBR] [4]
  promoter yaeQp6 214195 forward nd [ICWHO] [3]
  promoter TSS_394 214197 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_395 214269 forward nd [RS-EPT-CBR] [4]
  promoter TSS_396 215265 forward nd [RS-EPT-CBR] [4]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Kogure H., Handa Y., Nagata M., Kanai N., Guntert P., Kubota K., Nameki N., 2014, Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ., Nucleic Acids Res 42(5):3152-63

 [2] Ohtake K., Sato A., Mukai T., Hino N., Yokoyama S., Sakamoto K., 2012, Efficient decoding of the UAG triplet as a full-fledged sense codon enhances the growth of a prfA-deficient strain of Escherichia coli., J Bacteriol 194(10):2606-13

 [3] 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

 [4] 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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