1F0O

PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.205 

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:  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 cati ...

    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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TYPE II RESTRICTION ENZYME PVUII
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
(5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C-3')C,D13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.043α = 90.00
b = 84.702β = 90.00
c = 45.993γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description