4KIS

Crystal Structure of a LSR-DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Attachment site recognition and regulation of directionality by the serine integrases.

Rutherford, K.Yuan, P.Perry, K.Sharp, R.Van Duyne, G.D.

(2013) Nucleic Acids Res 41: 8341-8356

  • DOI: 10.1093/nar/gkt580
  • Primary Citation of Related Structures:  
    4KIS

  • PubMed Abstract: 
  • Serine integrases catalyze the integration of bacteriophage DNA into a host genome by site-specific recombination between 'attachment sites' in the phage (attP) and the host (attB). The reaction is highly directional; the reverse excision reaction be ...

    Serine integrases catalyze the integration of bacteriophage DNA into a host genome by site-specific recombination between 'attachment sites' in the phage (attP) and the host (attB). The reaction is highly directional; the reverse excision reaction between the product attL and attR sites does not occur in the absence of a phage-encoded factor, nor does recombination occur between other pairings of attachment sites. A mechanistic understanding of how these enzymes achieve site-selectivity and directionality has been limited by a lack of structural models. Here, we report the structure of the C-terminal domains of a serine integrase bound to an attP DNA half-site. The structure leads directly to models for understanding how the integrase-bound attP and attB sites differ, why these enzymes preferentially form attP × attB synaptic complexes to initiate recombination, and how attL × attR recombination is prevented. In these models, different domain organizations on attP vs. attB half-sites allow attachment-site specific interactions to form between integrase subunits via an unusual protruding coiled-coil motif. These interactions are used to preferentially synapse integrase-bound attP and attB and inhibit synapsis of integrase-bound attL and attR. The results provide a structural framework for understanding, testing and engineering serine integrase function.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative integrase [Bacteriophage A118]ABCD328Listeria innocua Clip11262Mutation(s): 0 
Gene Names: int
Find proteins for Q928V6 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262))
Explore Q928V6 
Go to UniProtKB:  Q928V6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (26-MER)F, H, J, L26N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (26-MER)E, G, I, K26N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B, C, D, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 290.75α = 90
b = 290.75β = 90
c = 290.75γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references