RegulonDB RegulonDB 10.9: Gene Form
   

xerD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

xerD dsbC fldB SoxS SoxS CpxR CpxR xerDp xerDp fldBp fldBp TSS_3168 TSS_3168 TSS_3167 TSS_3167 dsbCp2 dsbCp2 TSS_3166 TSS_3166 dsbCp dsbCp

Gene      
Name: xerD    Texpresso search in the literature
Synonym(s): ECK2889, EG11071, b2894, xprB
Genome position(nucleotides): 3038847 <-- 3039743 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.07
External database links:  
ASAP:
ABE-0009500
CGSC:
30201
ECHOBASE:
EB1064
ECOLIHUB:
xerD
OU-MICROARRAY:
b2894
STRING:
511145.b2894
COLOMBOS: xerD


Product      
Name: site-specific recombinase
Synonym(s): XerD, XprB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 34.246
Isoelectric point: 9.18
Motif(s):
 
Type Positions Sequence
2 -> 87 KQDLARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSARLLSAVRRLFQYLY
8 -> 90 IEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSARLLSAVRRLFQYLYREK
298 -> 298 A
108 -> 292 RLPKDLSEAQVERLLQAPLIDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQ
256 -> 258 NHG

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.3 - DNA recombination
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0048476 - Holliday junction resolvase complex
molecular_function GO:0003677 - DNA binding
GO:0009009 - site-specific recombinase activity
GO:0009037 - tyrosine-based site-specific recombinase activity
biological_process GO:0051301 - cell division
GO:0006276 - plasmid maintenance
GO:0006310 - DNA recombination
GO:0006313 - transposition, DNA-mediated
GO:0007049 - cell cycle
GO:0009314 - response to radiation
GO:0007059 - chromosome segregation
GO:0015074 - DNA integration
GO:0071139 - resolution of recombination intermediates
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Blakely G., et al., 1993
[2] Lovett ST., et al., 1991
External database links:  
DIP:
DIP-48125N
ECOCYC:
EG11071-MONOMER
ECOLIWIKI:
b2894
INTERPRO:
IPR002104
INTERPRO:
IPR023009
INTERPRO:
IPR013762
INTERPRO:
IPR011932
INTERPRO:
IPR011010
INTERPRO:
IPR004107
INTERPRO:
IPR010998
MODBASE:
P0A8P8
PDB:
1A0P
PFAM:
PF02899
PFAM:
PF00589
PRIDE:
P0A8P8
PRODB:
PRO_000024235
PROSITE:
PS51900
PROSITE:
PS51898
REFSEQ:
NP_417370
SMR:
P0A8P8
UNIPROT:
P0A8P8


Operon      
Name: xerD-dsbC-recJ-prfB-lysS         
Operon arrangement:
Transcription unit        Promoter
dsbC
dsbC-recJ-prfB
xerD-dsbC-recJ
xerD-dsbC-recJ
prfB-lysS
xerD


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_3166 3038872 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3167 3039766 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3168 3039778 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] Blakely G., May G., McCulloch R., Arciszewska LK., Burke M., Lovett ST., Sherratt DJ., 1993, Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12., Cell 75(2):351-61

 [2] Lovett ST., Kolodner RD., 1991, Nucleotide sequence of the Escherichia coli recJ chromosomal region and construction of recJ-overexpression plasmids., J Bacteriol 173(1):353-64

 [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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