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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. Sequential strand exchange by XerC and XerD during site-specific recombination at dif. Blakely GW, et al. J Biol Chem, 2000 Apr 7. PMID 10744667
    3. An efficient method of selectable marker gene excision by Xer recombination for gene replacement in bacterial chromosomes. Bloor AE, et al. Appl Environ Microbiol, 2006 Apr. PMID 16597952, Free PMC Article
    4. Action of site-specific recombinases XerC and XerD on tethered Holliday junctions. Arciszewska LK, et al. EMBO J, 1997 Jun 16. PMID 9218814, Free PMC Article
    5. Recombinase binding specificity at the chromosome dimer resolution site dif of Escherichia coli. Hayes F, et al. J Mol Biol, 1997 Feb 28. PMID 9067608

    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.
    Submit: New GeneRIF Correction

    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
    Heading Accession and Version

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