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xerD site-specific recombinase [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 947362, updated on 3-Dec-2024

Summary

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Official Symbol
xerD
Official Full Name
site-specific recombinase
Primary source
ECOCYC:EG11071
Locus tag
b2894
See related
ASAP:ABE-0009500
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as
ECK2889; xprB
Summary
XerCD acts at the Dif site. [More information is available at EcoGene: EG11071]. XerD is part of the Xer site-specific recombination system . [More information is available at EcoCyc: EG11071].
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Genomic context

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Sequence:
NC_000913.3 (3038847..3039743, complement)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene ssDNA-specific exonuclease RecJ Neighboring gene protein disulfide isomerase DsbC Neighboring gene flavodoxin 2 Neighboring gene protein YgfX Neighboring gene FAD assembly factor

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Relating primary structure to function in the Escherichia coli XerD site-specific recombinase. Spiers AJ, et al. Mol Microbiol, 1997 Jun. PMID 9220013
  2. DNA sequence of recombinase-binding sites can determine Xer site-specific recombination outcome. Blake JA, et al. Mol Microbiol, 1997 Jan. PMID 9044272
  3. Switching catalytic activity in the XerCD site-specific recombination machine. Ferreira H, et al. J Mol Biol, 2001 Sep 7. PMID 11545584
  4. Osmoregulation of dimer resolution at the plasmid pJHCMW1 mwr locus by Escherichia coli XerCD recombination. Pham H, et al. J Bacteriol, 2002 Mar. PMID 11872712, Free PMC Article
  5. Functional analysis of the C-terminal domains of the site-specific recombinases XerC and XerD. Ferreira H, et al. J Mol Biol, 2003 Jun 27. PMID 12818199

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FtsKgamma interacts with the C-terminal domain of XerD, above a cleft where XerC is thought to bind. We present a model for activation of recombination based on structural data.
    Title: Activation of Xer-recombination at dif: structural basis of the FtsKγ-XerD interaction.
  2. e reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle.
    Title: Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome.
  3. FtsK translocase has a role in assembly, translocation, and activation of XerCD-dif recombination
    Title: Assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion.
  4. Data indicate that the arrival of the FtsK translocase at an initial synaptic complex, forming a transient activated complex in which XerD exchanged a pair of strands to form an Holliday junctions (HJ) intermediate for catalysis by XerC.
    Title: Conformational transitions during FtsK translocase activation of individual XerCD-dif recombination complexes.
  5. N-terminus verified by Edman degradation on complete protein
    Title: Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12.
  6. A 62-amino-acid fragment of FtsK(C) interacts directly with the XerD C-terminus in order to stimulate the cleavage by XerD of BSN, a dif-DNA suicide substrate containing a nick in the 'bottom' strand.
    Title: Dissection of a functional interaction between the DNA translocase, FtsK, and the XerD recombinase.
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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables site-specific recombinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables site-specific recombinase activity IEA
Inferred from Electronic Annotation
more info
  
enables tyrosine-based site-specific recombinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables tyrosine-based site-specific recombinase activity IEA
Inferred from Electronic Annotation
more info
  
enables tyrosine-based site-specific recombinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA integration IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA transposition IEA
Inferred from Electronic Annotation
more info
  
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in chromosome segregation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromosome segregation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromosome segregation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within plasmid maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in resolution of DNA recombination intermediates IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within resolution of DNA recombination intermediates IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in resolution of DNA recombination intermediates IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within response to radiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Holliday junction resolvase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Holliday junction resolvase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
site-specific recombinase

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_000913.3 Reference assembly

    Range
    3038847..3039743 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_417370.1 site-specific recombinase [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_417370.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A376FVC9
    Conserved Domains (1) summary
    PRK00283
    Location:1 → 298
    xerD; tyrosine recombinase
Nucleotide Protein
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