2A3V

Structural basis for broad DNA-specificity in integron recombination

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

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This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for broad DNA-specificity in integron recombination.

MacDonald, D., Demarre, G., Bouvier, M., Mazel, D., Gopaul, D.N.

(2006) Nature 440: 1157-1162

  • DOI: 10.1038/nature04643
  • Primary Citation of Related Structures:  
    2A3V

  • PubMed Abstract: 

    • Lateral DNA transfer--the movement of genetic traits between bacteria--has a profound impact on genomic evolution and speciation. The efficiency with which bacteria incorporate genetic information reflects their capacity to adapt to changing environmental conditions ...

    Lateral DNA transfer--the movement of genetic traits between bacteria--has a profound impact on genomic evolution and speciation. The efficiency with which bacteria incorporate genetic information reflects their capacity to adapt to changing environmental conditions. Integron integrases are proteins that mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. The lack of sequence conservation among attC sites has led to the hypothesis that a sequence-independent structural recognition determinant must exist within attC. Here we report the crystal structure of an integron integrase bound to an attC substrate. The structure shows that DNA target site recognition and high-order synaptic assembly are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. These extrahelical bases, one of which is required for recombination in vivo, originate from folding of the bottom strand of attC owing to its imperfect internal dyad symmetry. The mechanism reported here supports a new paradigm for how sequence-degenerate single-stranded genetic material is recognized and exchanged between bacteria.

    Organizational Affiliation: 

    Laboratoire de Biochimie et Biophysique des Macromolécules, Département de Biologie Structurale et Chimie, CNRS URA 2171, Institut Pasteur, 75724 Paris Cedex 15, France.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
site-specific recombinase IntI4E [auth A], F [auth B], G [auth C], H [auth D]320Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 1 
Gene Names: intI4
Find proteins for O68847 (Vibrio cholerae)
Explore O68847 
Go to UniProtKB:  O68847
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (31-MER)A [auth E], C [auth G]40N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (34-MER)B [auth F], D [auth H]43N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.9α = 90
b = 170.2β = 90
c = 209.4γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SnBphasing
CNSrefinement
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description