1BUA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.200 

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 Biol 6: 269-276

  • 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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ENDONUCLEASE ECORVC [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
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*AP*GP*AP*CP*IP*TP*CP*TP*T)-3')A [auth C], B [auth D]11N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.15 Å
    • R-Value Free: 0.288 
    • R-Value Work: 0.200 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 50.3α = 109.3
    b = 64.2β = 108.3
    c = 49.4γ = 96.3
    Software Package:
    Software NamePurpose
    X-PLORmodel building
    X-PLORrefinement
    R-AXISdata reduction
    R-AXISdata scaling
    X-PLORphasing

    Structure Validation

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    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