3UXP

Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta.

Gridley, C.L.Rangarajan, S.Firbank, S.Dalal, S.Sweasy, J.B.Jaeger, J.

(2013) Biochemistry 52: 4422-4432

  • DOI: 10.1021/bi301368f
  • Primary Citation of Related Structures:  
    3UXN, 3UXO, 3UXP

  • PubMed Abstract: 
  • The I260Q variant of DNA polymerase β is an efficient mutator polymerase with fairly indiscriminate misincorporation activities opposite all template bases. Previous modeling studies have suggested that I260Q harbors structural variations in its hinge region ...

    The I260Q variant of DNA polymerase β is an efficient mutator polymerase with fairly indiscriminate misincorporation activities opposite all template bases. Previous modeling studies have suggested that I260Q harbors structural variations in its hinge region. Here, we present the crystal structures of wild type and I260Q rat polymerase β in the presence and absence of substrates. Both the I260Q apoenzyme structure and the closed ternary complex with double-stranded DNA and ddTTP show ordered water molecules in the hydrophobic hinge near Gln260, whereas this is not the case in the wild type polymerase. Compared to wild type polymerase β ternary complexes, there are subtle movements around residues 260, 272, 295, and 296 in the mutant. The rearrangements in this region, coupled with side chain movements in the immediate neighborhood of the dNTP-binding pocket, namely, residues 258 and 272, provide an explanation for the altered activity and fidelity profiles observed in the I260Q mutator polymerase.


    Organizational Affiliation

    Division of Genetics, Wadsworth Center, New York State Department of Health, New Scotland Avenue, Albany, New York 12208, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase beta AB335Rattus norvegicusMutation(s): 1 
Gene Names: Polb
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for P06766 (Rattus norvegicus)
Explore P06766 
Go to UniProtKB:  P06766
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'D, P7N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'E, T9N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.72 Å
      • R-Value Free: 0.292 
      • R-Value Work: 0.218 
      • R-Value Observed: 0.225 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 100.321α = 90
      b = 56.607β = 102.04
      c = 93.144γ = 90
      Software Package:
      Software NamePurpose
      CBASSdata collection
      PHASERphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-12-05
        Type: Initial release
      • Version 1.1: 2013-08-28
        Changes: Database references