RegulonDB RegulonDB 11.1: Gene Form
   

recD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

recB ptrA recD argA TSS_3127 TSS_3127

Gene      
Name: recD    Texpresso search in the literature
Synonym(s): ECK2815, EG10826, b2819, hopE
Genome position(nucleotides): 2950635 <-- 2952461
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.28
External database links:  
ASAP:
 ABE-0009247
CGSC:
 4975
ECHOBASE:
 EB0819
ECOLIHUB:
 recD
OU-MICROARRAY:
 b2819
STRING:
 511145.b2819
COLOMBOS: recD


Product      
Name: exodeoxyribonuclease V subunit RecD
Synonym(s): HopE, RecD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 66.902
Isoelectric point: 7.015
Motif(s):
 
Type Positions Sequence Comment
156 -> 319 VAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDALPDHARVIFLGDRDQLASVEAGAVLGDICAYANA
171 -> 178 GGPGTGKT UniProt: ATP.
177 -> 177 K UniProt: Loss of ATP-dependent exonuclease activity in holoenzyme. Subunit loses ATPase and has ~5% 5'-3' helicase activity, holoenzyme has 2-4 fold less helicase activity, 5-fold less processivity..
247 -> 248 QP UniProt: In Ref. 1; CAA28253..
306 -> 306 A UniProt: In Ref. 1; CAA28253..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.2 - DNA
  2 - information transfer --> 2.1 - DNA related --> 2.1.3 - DNA recombination
  2 - information transfer --> 2.1 - DNA related --> 2.1.5 - DNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0009338 - exodeoxyribonuclease V complex
molecular_function GO:0043139 - 5'-3' DNA helicase activity
GO:0003677 - DNA binding
GO:0003678 - DNA helicase activity
GO:0004386 - helicase activity
GO:0004518 - nuclease activity
GO:0004527 - exonuclease activity
GO:0016787 - hydrolase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0008854 - exodeoxyribonuclease V activity
GO:0017116 - single-stranded DNA helicase activity
biological_process GO:0006281 - DNA repair
GO:0006310 - DNA recombination
GO:0006974 - cellular response to DNA damage stimulus
GO:0032508 - DNA duplex unwinding
GO:0000725 - recombinational repair
GO:0006302 - double-strand break repair
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0000724 - double-strand break repair via homologous recombination
Note(s): Note(s): ...[more].
Reference(s): [1] Biek DP., et al., 1986
[2] Dermic D. 2006
External database links:  
ALPHAFOLD:
 P04993
DIP:
 DIP-10651N
ECOCYC:
 EG10826-MONOMER
ECOLIWIKI:
 b2819
INTERPRO:
 IPR027785
INTERPRO:
 IPR041851
INTERPRO:
 IPR027417
INTERPRO:
 IPR006344
INTERPRO:
 IPR003593
MINT:
 P04993
MODBASE:
 P04993
PDB:
 6T2V
PDB:
 6SJE
PDB:
 5MBV
PDB:
 6SJF
PDB:
 3K70
PDB:
 6SJG
PDB:
 6T2U
PDB:
 6SJB
PDB:
 1W36
PDB:
 5LD2
PFAM:
 PF13604
PFAM:
 PF13538
PRIDE:
 P04993
PRODB:
 PRO_000023699
REFSEQ:
 NP_417296
SMART:
 SM00382
SMR:
 P04993
UNIPROT:
 P04993


Operon      
Name: ptrA-recBD         
Operon arrangement:
Transcription unit        Promoter
ptrA
ptrA-recBD


Transcriptional Regulation      
Display Regulation             
Repressed by: 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 TSS_3127 2951765 reverse nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Biek DP., Cohen SN., 1986, Identification and characterization of recD, a gene affecting plasmid maintenance and recombination in Escherichia coli., J Bacteriol 167(2):594-603

 [2] Dermic D., 2006, Functions of multiple exonucleases are essential for cell viability, DNA repair and homologous recombination in recD mutants of Escherichia coli., Genetics 172(4):2057-69

 [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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