1BSU

STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.

Martin, A.M.Sam, M.D.Reich, N.O.Perona, J.J.

(1999) Nat.Struct.Mol.Biol. 6: 269-277

  • DOI: 10.1038/6707
  • Primary Citation of Related Structures:  1BUA

  • PubMed Abstract: 
  • Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this posit ...

    Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.


    Related Citations: 
    • Metal Ion Mediated Substrate-Assisted Catalysis in Type II Restriction Endonucleases
      Horton, N.C.,Perona, J.J.
      (1998) Proc.Natl.Acad.Sci.USA 95: 13489
    • Conformational Transitions and Structural Deformability of EcoRV Endonuclease Revealed by Crystallographic Analysis
      Perona, J.J.,Martin, A.M.
      (1997) J.Mol.Biol. 273: 207


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ENDONUCLEASE ECORV (3.1.21.4)
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(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3')C10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3')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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C, D
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.183 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.300α = 109.10
b = 64.000β = 108.10
c = 49.100γ = 96.50
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
R-AXISdata scaling
R-AXISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-09
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance