Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.68 kDa 
• Atom Count: 3096 
• Modelled Residue Count: 338 
• Deposited Residue Count: 340 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1PVI

STRUCTURE OF PVUII ENDONUCLEASE WITH COGNATE DNA

• PDB DOI: 10.2210/pdb1PVI/pdb
• NDB: PDE017

• Classification: HYDROLASE/DNA
• Organism(s): Proteus vulgaris
• Mutation(s): No 


• Deposited: 1994-11-16 Released: 1995-02-14 
• Deposition Author(s): Cheng, X., Balendiran, K., Schildkraut, I., Anderson, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

Structure of PvuII endonuclease with cognate DNA.

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

(1994) EMBO J 13: 3927-3935

• PubMed: 8076590 
• Primary Citation of Related Structures:  
  1PVI


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PVUII (E.C.3.1.21.4))	C [auth A], D [auth B]	157	Proteus vulgaris	Mutation(s): 0  EC: 3.1.21.4
UniProt
Find proteins for P23657 (Proteus hauseri) Explore P23657  Go to UniProtKB:  P23657

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')	A [auth C], B [auth D]	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.8	α = 90
b = 86.3	β = 90
c = 48.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
MADNES	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-11-16 
• Released Date: 1995-02-14 
Deposition Author(s): Cheng, X., Balendiran, K., Schildkraut, I., Anderson, J.E.

Revision History  

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