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: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 Biol 6: 269-277

  • DOI: 10.1038/6707
  • Primary Citation of Related Structures:  
    1BSU, 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 position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout ...

    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 U S A 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:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ENDONUCLEASE ECORV (3.1.21.4)C [auth A], D [auth B]244Escherichia coliMutation(s): 0 
Gene Names: ecoRVR
EC: 3.1.21.4
UniProt
Find proteins for P04390 (Escherichia coli)
Explore P04390 
Go to UniProtKB:  P04390
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3')A [auth C]10N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3')B [auth D]11N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      E [auth A], F [auth B]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.00 Å
      • R-Value Free: 0.258 
      • R-Value Work: 0.183 
      • R-Value Observed: 0.183 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 50.3α = 109.1
      b = 64β = 108.1
      c = 49.1γ = 96.5
      Software Package:
      Software NamePurpose
      X-PLORmodel building
      X-PLORrefinement
      R-AXISdata reduction
      R-AXISdata scaling
      X-PLORphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1998-09-09
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2019-11-20
        Changes: Derived calculations