1RV5

COMPLEX OF ECORV ENDONUCLEASE WITH D(AAAGAT)/D(ATCTT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.

(1998) J.Mol.Biol. 277: 779-783

  • DOI: 10.1006/jmbi.1998.1655

  • PubMed Abstract: 
  • The crystal structure of EcoRV endonuclease has been determined at 2. 1 A resolution complexed to two five-base-pair DNA duplexes each containing the cognate recognition half-site. The highly localized 50 degrees bend into the major groove seen at th ...

    The crystal structure of EcoRV endonuclease has been determined at 2. 1 A resolution complexed to two five-base-pair DNA duplexes each containing the cognate recognition half-site. The highly localized 50 degrees bend into the major groove seen at the center TA-step of the continuous GATATC site is preserved in this discontinuous DNA complex lacking the scissile phosphates. Thus, this crystal structure provides evidence that covalent constraints associated with a continuous target site are not essential to enzyme-induced DNA bending, even when these constraints are removed directly at the locus of the bend. The scissile phosphates are also absent in the crystal structure of EcoRV bound to the non-specific site TCGCGA, which shows a straight B-like conformation. We conclude that DNA bending by EcoRV is governed only by the sequence and is not influenced by the continuity of the phosphodiester backbone. Together with other data showing that cleavable non-cognate sites are bent, these results indicate that EcoRV bends non-cognate sites differing by one or two base-pairs from GATATC, but does not bend non-specific sites that are less similar. Structural and thermodynamic considerations suggest that the sequence-dependent energy cost of DNA bending is likely to play an important role in determining the specificity of EcoRV. This differential cost is manifested at the binding step for bent non-cognate sequences and at the catalytic step for unbent non-specific sequences.


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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ECORV ENDONUCLEASE
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
5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'C,D11N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.600α = 96.40
b = 50.400β = 109.20
c = 63.900γ = 108.50
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance