1PVI

STRUCTURE OF PVUII ENDONUCLEASE WITH COGNATE DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of PvuII endonuclease with cognate DNA.

Cheng, X.Balendiran, K.Schildkraut, I.Anderson, J.E.

(1994) EMBO J. 13: 3927-3935


  • PubMed Abstract: 
  • We have determined the structure of PvuII endonuclease complexed with cognate DNA by X-ray crystallography. The DNA substrate is bound with a single homodimeric protein, each subunit of which reveals three structural regions. The catalytic region str ...

    We have determined the structure of PvuII endonuclease complexed with cognate DNA by X-ray crystallography. The DNA substrate is bound with a single homodimeric protein, each subunit of which reveals three structural regions. The catalytic region strongly resembles structures of other restriction endonucleases, even though these regions have dissimilar primary sequences. Comparison of the active site with those of EcoRV and EcoRI endonucleases reveals a conserved triplet sequence close to the reactive phosphodiester group and a conserved acidic pair that may represent the ligands for the catalytic cofactor Mg2+. The DNA duplex is not significantly bent and maintains a B-DNA-like conformation. The subunit interface region of the homodimeric protein consists of a pseudo-three-helix bundle. Direct contacts between the protein and the base pairs of the PvuII recognition site occur exclusively in the major groove through two antiparallel beta strands from the sequence recognition region of the protein. Water-mediated contacts are made in the minor grooves to central bases of the site. If restriction enzymes do share a common ancestor, as has been proposed, their catalytic regions have been very strongly conserved, while their subunit interfaces and DNA sequence recognition regions have undergone remarkable structural variation.


    Related Citations: 
    • Expression, Purification, and Crystallization of Restriction Endonuclease PvuII with DNA Containing its Recognition Site
      Balendiran, K.,Bonventre, J.,Knott, R.,Jack, W.,Benner, J.,Schildkraut, I.,Anderson, J.E.
      (1994) Proteins 19: 77


    Organizational Affiliation

    W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, NY 11724.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PVUII (E.C.3.1.21.4))
A, B
157Proteus hauseriGene Names: pvuIIR
EC: 3.1.21.4
Find proteins for P23657 (Proteus hauseri)
Go to UniProtKB:  P23657
Entity ID: 1
MoleculeChainsLengthOrganism
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: 2.6 Å
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.800α = 90.00
b = 86.300β = 90.00
c = 48.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
MADNESdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance