2GE5

EcoRV Restriction Endonuclease C-terminal deletion mutant/GATATC/Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Positively Charged C-Terminal Subdomains of EcoRV Endonuclease: Contributions to DNA Binding, Bending, and Cleavage.

Hiller, D.A.Perona, J.J.

(2006) Biochemistry 45: 11453-11463

  • DOI: 10.1021/bi0606400

  • PubMed Abstract: 
  • The carboxy-terminal subdomains of the homodimeric EcoRV restriction endonuclease each bear a net charge of +4 and are positioned on the inner concave surface of the 50 degree DNA bend that is induced by the enzyme. A complete kinetic and structural ...

    The carboxy-terminal subdomains of the homodimeric EcoRV restriction endonuclease each bear a net charge of +4 and are positioned on the inner concave surface of the 50 degree DNA bend that is induced by the enzyme. A complete kinetic and structural analysis of a truncated EcoRV mutant lacking these domains was performed to assess the importance of this diffuse charge in facilitating DNA binding, bending, and cleavage. At the level of formation of an enzyme-DNA complex, the association rate for the dimeric mutant enzyme was sharply decreased by 10(3)-fold, while the equilibrium dissociation constant was weakened by nearly 10(6)-fold compared with that of wild-type EcoRV. Thus, the C-terminal subdomains strongly stabilize the enzyme-DNA ground-state complex in which the DNA is known to be bent. Further, the extent of DNA bending as observed by fluorescence resonance energy transfer was also significantly decreased. The crystal structure of the truncated enzyme bound to DNA and calcium ions at 2.4 A resolution reveals that the global fold is preserved and suggests that a divalent metal ion crucial to catalysis is destabilized in the active site. This may explain the 100-fold decrease in the rate of metal-dependent phosphoryl transfer observed for the mutant. These results show that diffuse positive charge associated with the C-terminal subdomains of EcoRV plays a key role in DNA association, bending, and cleavage.


    Related Citations: 
    • Crystallographic snapshots along a protein-induced DNA-bending pathway
      Horton, N.C.,Perona, J.J.
      (2000) Proc.Natl.Acad.Sci.USA 97: 5729
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Type II restriction enzyme EcoRV
A, B
219Escherichia coliMutation(s): 0 
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: 2.4 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.101α = 90.00
b = 67.101β = 90.00
c = 259.892γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
PDB_EXTRACTdata extraction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance