1Q9Y

CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE
A
906Escherichia 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)
Go to UniProtKB:  Q38087
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3'T18N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3'P14N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

Download CCD File 
P
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.822α = 90
b = 118.565β = 90
c = 127.224γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction

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: Version format compliance