1CW0

CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.

Tsutakawa, S.E.Jingami, H.Morikawa, K.

(1999) Cell 99: 615-623

  • DOI: 10.1016/s0092-8674(00)81550-0
  • Primary Citation of Related Structures:  
    1CW0

  • PubMed Abstract: 
  • The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine ...

    The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine. Extensive interactions between the DNA and the protein characterize a novel recognition mechanism, where three aromatic residues intercalate from the major groove into the DNA to strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides detailed insights into the catalytic mechanism for endonuclease activity.


    Organizational Affiliation

    Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DNA MISMATCH ENDONUCLEASE)D [auth A]155Escherichia coliMutation(s): 0 
EC: 3.1
Find proteins for P09184 (Escherichia coli (strain K12))
Explore P09184 
Go to UniProtKB:  P09184
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)-3')A [auth M]12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*GP*C)-3')B [auth N]3N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3')C [auth O]9N/A
        Small Molecules
        Ligands 2 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        ZN
        Query on ZN

        Download Ideal Coordinates CCD File 
        F [auth A]ZINC ION
        Zn
        PTFCDOFLOPIGGS-UHFFFAOYSA-N
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        E [auth N], G [auth A]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.30 Å
        • R-Value Free: 0.230 
        • R-Value Work: 0.204 
        • R-Value Observed: 0.204 
        • Space Group: P 65
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 63α = 90
        b = 63β = 90
        c = 152.5γ = 120
        Software Package:
        Software NamePurpose
        AMoREphasing
        CNSrefinement
        DENZOdata reduction
        SCALEPACKdata scaling

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 1999-12-12
          Type: Initial release
        • Version 1.1: 2008-04-27
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance