RegulonDB RegulonDB 11.1: Gene Form
   

rpnC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpnC panC panD GcvB TSS_271 TSS_271 yadDp4 yadDp4 yadDp5 yadDp5 yadDp3 yadDp3 panDp2 panDp2 panDp1 panDp1

Gene      
Name: rpnC    Texpresso search in the literature
Synonym(s): ECK0131, EG11748, b0132, yadD
Genome position(nucleotides): 146968 --> 147870
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.84
External database links:  
ASAP:
 ABE-0000463
ECHOBASE:
 EB1698
ECOLIHUB:
 yadD
OU-MICROARRAY:
 b0132
STRING:
 511145.b0132
COLOMBOS: rpnC


Product      
Name: recombination-promoting nuclease RpnC
Synonym(s): RpnC, YadD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 34.607
Isoelectric point: 5.092
Motif(s):
 
Type Positions Sequence Comment
7 -> 207 TPHDAVFKQFLMHAETARDFLEIHLPVELRELCDLNTLHLESGSFIEESLKGHSTDVLYSVQMQGNPGYLHVVIEHQSKPDKKMAFRMMRYSIAAMHRHLEADHDKLPLVVPILFYQGEATPYPLSMCWFDMFYSPELARRVYNSPFPLVDITITPDDEIMQHRRIAILELLQKHIRQRDLMLLLEQLVTLIDEGYTSGSQ

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.4 - genetic exchange, recombination (for future)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0016787 - hydrolase activity
GO:1990238 - double-stranded DNA endodeoxyribonuclease activity
biological_process GO:0006310 - DNA recombination
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Kingston AW., et al., 2017
[2] Meydan S., et al., 2019
External database links:  
ALPHAFOLD:
 P31665
ECOCYC:
 EG11748-MONOMER
ECOLIWIKI:
 b0132
INTERPRO:
 IPR006842
INTERPRO:
 IPR010106
PFAM:
 PF04754
PRIDE:
 P31665
REFSEQ:
 NP_414674
SMR:
 P31665
UNIPROT:
 P31665


Operon      
Name: rpnC         
Operon arrangement:
Transcription unit        Promoter
yadD


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 yadDp3 146898 forward nd [COMP-AINF] [3]
  promoter yadDp5 146957 forward nd [COMP-AINF] [3]
  promoter yadDp4 146959 forward nd [COMP-AINF] [3]
  promoter TSS_271 147583 forward nd [RS-EPT-CBR] [4]


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] Kingston AW., Ponkratz C., Raleigh EA., 2017, Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer., J Bacteriol 199(7)

 [2] Meydan S., Marks J., Klepacki D., Sharma V., Baranov PV., Firth AE., Margus T., Kefi A., Vazquez-Laslop N., Mankin AS., 2019, Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome., Mol Cell 74(3):481-493.e6

 [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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