1Q9X

Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Lesion (in)tolerance reveals insights into DNA replication fidelity.

Freisinger, E.Grollman, A.P.Miller, H.Kisker, C.

(2004) EMBO J 23: 1494-1505

  • DOI: 10.1038/sj.emboj.7600158
  • Primary Citation of Related Structures:  
    1Q9X, 1Q9Y

  • PubMed Abstract: 
  • The initial encounter of an unrepaired DNA lesion is likely to be with a replicative DNA polymerase, and the outcome of this event determines whether an error-prone or error-free damage avoidance pathway is taken. To understand the atomic details of ...

    The initial encounter of an unrepaired DNA lesion is likely to be with a replicative DNA polymerase, and the outcome of this event determines whether an error-prone or error-free damage avoidance pathway is taken. To understand the atomic details of this critical encounter, we have determined the crystal structures of the pol alpha family RB69 DNA polymerase with DNA containing the two most prevalent, spontaneously generated premutagenic lesions, an abasic site and 2'-deoxy-7,8-dihydro-8-oxoguanosine (8-oxodG). Identification of the interactions between these damaged nucleotides and the active site provides insight into the capacity of the polymerase to incorporate a base opposite the lesion. A novel open, catalytically inactive conformation of the DNA polymerase has been identified in the complex with a primed abasic site template. This structure provides the first molecular characterization of the DNA synthesis barrier caused by an abasic site and suggests a general mechanism for polymerase fidelity. In contrast, the structure of the ternary 8-oxodG:dCTP complex is almost identical to the replicating complex containing unmodified DNA, explaining the relative ease and fidelity by which this lesion is bypassed.


    Organizational Affiliation

    Department of Pharmacological Sciences, Center for Structural Biology, SUNY at Stony Brook, Stony Brook, NY, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseABCD903Escherichia phage RB69Mutation(s): 2 
Gene Names: 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-GCGGACTGCTTAC(dideoxycytidine)-3'E, F, G, H18N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-AC(tetrahydrofuran)GGTAAGCAGTCCGCGG-3'I, J, K, L13N/A
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DGP
      Query on DGP

      Download CCD File 
      F, G, H, K, L
      2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
      C10 H14 N5 O7 P
      LTFMZDNNPPEQNG-KVQBGUIXSA-N
       Ligand Interaction
      DOC
      Query on DOC

      Download CCD File 
      I, J, K, L
      2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
      C9 H14 N3 O6 P
      RAJMXAZJKUGYGW-POYBYMJQSA-N
       Ligand Interaction
      3DR
      Query on 3DR

      Download CCD File 
      E, F, G, H
      1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
      C5 H11 O6 P
      BVOBPNSQIRMLCA-CRCLSJGQSA-N
       Ligand Interaction
      CA
      Query on CA

      Download CCD File 
      A, B, C, D
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.69 Å
      • R-Value Free: 0.288 
      • R-Value Work: 0.215 
      • R-Value Observed: 0.219 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 131.948α = 90
      b = 122.237β = 96.85
      c = 165.358γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      MOLREPphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-04-27
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Non-polymer description, Version format compliance