1BSS

ECORV-T93A/DNA/CA2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases

Horton, N.C.Newberry, K.J.Perona, J.J.

(1998) Proc.Natl.Acad.Sci.USA 95: 13489-13494


  • PubMed Abstract: 
  • The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the ph ...

    The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3' to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile.


    Related Citations: 
    • Conformational Transitions and Structural Deformability of EcoRV Endonuclease Revealed by Crystallographic Analysis
      Perona, J.J.,Martin, A.M.
      (1997) J.Mol.Biol. 273: 207
    • Role of Protein-induced Bending in the Specificity of DNA Recognition: Crystal Structure of EcoRV Endonuclease Complexed with d(AAAGAT + d(ATCTT)
      Horton, N.C.,Perona, J.J.
      (1997) J.Mol.Biol. 277: 779


    Organizational Affiliation

    Department of Chemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, CA 93106-9510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ECORV ENDONUCLEASE
A, B
244Escherichia coliMutation(s): 1 
Gene Names: ecoRVR
EC: 3.1.21.4
Find proteins for P04390 (Escherichia coli)
Go to UniProtKB:  P04390
Entity ID: 1
MoleculeChainsLengthOrganism
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
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.000α = 109.20
b = 64.400β = 108.70
c = 49.200γ = 95.80
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-02
    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