1B95

ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.206 

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This is version 1.2 of the entry. See complete history


Literature

Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group.

Thomas, M.P.Brady, R.L.Halford, S.E.Sessions, R.B.Baldwin, G.S.

(1999) Nucleic Acids Res 27: 3438-3445

  • DOI: 10.1093/nar/27.17.3438
  • Primary Citation of Related Structures:  
    1B94, 1B95, 1B96, 1B97

  • PubMed Abstract: 
  • Following random mutagenesis of the Eco RV endonuclease, a high proportion of the null mutants carry substitutions at Gln69. Such mutants display reduced rates for the DNA cleavage step in the reaction pathway, yet the crystal structures of wild-type Eco RV fail to explain why Gln69 is crucial for activity ...

    Following random mutagenesis of the Eco RV endonuclease, a high proportion of the null mutants carry substitutions at Gln69. Such mutants display reduced rates for the DNA cleavage step in the reaction pathway, yet the crystal structures of wild-type Eco RV fail to explain why Gln69 is crucial for activity. In this study, crystal structures were determined for two mutants of Eco RV, with Leu or Glu at residue 69, bound to specific DNA. The structures of the mutants are similar to the native protein and no function can be ascribed to the side chain of the amino acid at this locus. Instead, the structures of the mutant proteins suggest that the catalytic defect is due to the positioning of the main chain carbonyl group. In the enzyme-substrate complex for Eco RV, the main chain carbonyl of Gln69 makes no interactions with catalytic functions but, in the enzyme-product complex, it coordinates a metal ion bound to the newly liberated 5'-phosphate. This re-positioning may be hindered in the mutant proteins. Molecular dynamics calculations indicate that the metal on the phosphoryl oxygen interacts with the carbonyl group upon forming the pentavalent intermediate during phosphodiester hydrolysis. A main chain carbonyl may thus play a role in catalysis by Eco RV.


    Organizational Affiliation

    Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RESTRICTION 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*TP*AP*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: 2.05 Å
    • R-Value Free: 0.282 
    • R-Value Work: 0.206 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 48.48α = 97.03
    b = 48.63β = 108.87
    c = 63.86γ = 107.03
    Software Package:
    Software NamePurpose
    AMoREphasing
    REFMACrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1999-02-26
      Type: Initial release
    • Version 1.1: 2008-04-26
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance