1EYU

HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

PvuII endonuclease contains two calcium ions in active sites.

Horton, J.R.Cheng, X.

(2000) J Mol Biol 300: 1049-1056

  • DOI: 10.1006/jmbi.2000.3938
  • Primary Citation of Related Structures:  
    1F0O, 1EYU

  • PubMed Abstract: 
  • Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+) ...

    Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex, determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all structurally examined endonucleases, while the second position is similar to that of EcoRV but is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen leaving group. However, the interactions between the DNA scissile phosphate and the metals, the first metal and the attacking water, and the attacking water and DNA are the same in PvuII as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed three-metal or the two-metal models of EcoRV.


    Related Citations: 
    • Asp34 of PvuII Endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis
      Horton, J.R., Nastri, H.G., Riggs, P.D., Cheng, X.
      (1998) J Mol Biol 284: 1491
    • How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
      Horton, J.R., Bonventre, J., Cheng, X.
      (1998) Biol Chem 379: 451

    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TYPE II RESTRICTION ENZYME PVUIIAB157Proteus vulgarisMutation(s): 0 
EC: 3.1.21.4
Find proteins for P23657 (Proteus hauseri)
Explore P23657 
Go to UniProtKB:  P23657
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')C, D13N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.78 Å
    • R-Value Free: 0.243 
    • R-Value Work: 0.208 
    • R-Value Observed: 0.240 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 93.797α = 90
    b = 84.336β = 90
    c = 46.155γ = 90
    Software Package:
    Software NamePurpose
    X-PLORmodel building
    X-PLORrefinement
    SCALEPACKdata scaling
    X-PLORphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2000-07-21
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-10-04
      Changes: Refinement description