1AZ0

ECORV ENDONUCLEASE/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis.

Perona, J.J.Martin, A.M.

(1997) J.Mol.Biol. 273: 207-225

  • DOI: 10.1006/jmbi.1997.1315
  • Primary Citation of Related Structures:  1AZ3, 1AZ4

  • PubMed Abstract: 
  • The structures of wild-type and mutant forms of the unliganded EcoRV endonuclease dimer have been determined at 2.4 A resolution in a new crystal lattice. Comparison of these structures with that of the free enzyme determined with different packing c ...

    The structures of wild-type and mutant forms of the unliganded EcoRV endonuclease dimer have been determined at 2.4 A resolution in a new crystal lattice. Comparison of these structures with that of the free enzyme determined with different packing constraints shows that the conformations of the domain interfaces are not conserved between crystal forms. The unliganded enzyme and the enzyme-DNA complex delineate two distinct quaternary states separated by a 25 degrees intersubunit rotation, but considerable conformational heterogeneity, of the order of 10 degrees domain rotations, exists within each of these states. Comparison of the free enzyme structure between the two crystal forms further reveals that the C-terminal 28 amino acid residues are disordered and undergo an extensive local folding transition upon DNA binding. Introduction of the mutation T93A at the DNA-binding cleft causes large-scale effects on the protein conformation. Structural changes in the mutated unliganded enzyme propagate some 20 to 25 A to the dimerization interface and lead to a rearrangement of monomer subunits. Comparative analysis of these structures, a new structure of the enzyme cocrystallized with DNA and calcium ions, and previously determined cocrystal structures suggests important roles for a number of amino acid residues in facilitating the intersubunit motions and local folding transitions. In particular, the T93A structure reveals a pathway through the protein, by which DNA-binding may cause the domain movements required for proper alignment of catalytic groups. The key active-site residue Glu45 is located on a flexible helix inside this pathway, and this provides a direct means by which essential catalytic functions are coupled to the protein conformational change. It appears that indirect perturbation of the Glu45 conformation via an altered quaternary structure may be a contributing factor to the decreased catalytic efficiency of T93A, and this mechanism may also explain the diminished activities of other active site variants of EcoRV.


    Related Citations: 
    • The Crystal Structure of EcoRV Endonuclease and of its Complexes with Cognate and Non-Cognate DNA Fragments
      Winkler, F.K.,Banner, D.W.,Oefner, C.,Tsernoglou, D.,Brown, R.S.,Heathman, S.P.,Bryan, R.K.,Martin, P.D.,Petratos, K.,Wilson, K.S.
      (1993) Embo J. 12: 1781
    • Structure and Function of Restriction Endonucleases
      Winkler, F.K.
      (1992) Curr.Opin.Struct.Biol. 2: 93


    Organizational Affiliation

    Department of Chemistry, University of California at Santa Barbara 93106-9510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (TYPE II RESTRICTION ENZYME ECORV)
A, B
244Escherichia coliGene Names: ecoRVR
EC: 3.1.21.4
Find proteins for P04390 (Escherichia coli)
Go to UniProtKB:  P04390
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3')C,D11N/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 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.000α = 109.00
b = 50.200β = 108.00
c = 64.100γ = 96.00
Software Package:
Software NamePurpose
DENZOdata reduction
R-AXISdata scaling
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-19
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance