2DY4

Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.

Aller, P.Rould, M.A.Hogg, M.Wallace, S.S.Doublie, S.

(2007) Proc.Natl.Acad.Sci.USA 104: 814-818

  • DOI: 10.1073/pnas.0606648104
  • Also Cited By: 3RMD, 3RMC, 3RMB, 3RMA

  • PubMed Abstract: 
  • Thymine glycol (Tg) is a common product of oxidation and ionizing radiation, including that used for cancer treatment. Although Tg is a poor mutagenic lesion, it has been shown to present a strong block to both repair and replicative DNA polymerases. ...

    Thymine glycol (Tg) is a common product of oxidation and ionizing radiation, including that used for cancer treatment. Although Tg is a poor mutagenic lesion, it has been shown to present a strong block to both repair and replicative DNA polymerases. The 2.65-A crystal structure of a binary complex of the replicative RB69 DNA polymerase with DNA shows that the templating Tg is intrahelical and forms a regular Watson-Crick base pair with the incorporated A. The C5 methyl group protrudes axially from the ring of the damaged pyrimidine and hinders stacking of the adjacent 5' template guanine. The position of the displaced 5' template guanine is such that the next incoming nucleotide cannot be incorporated into the growing primer strand, and it explains why primer extension past the lesion is prohibited even though DNA polymerases can readily incorporate an A across from the Tg lesion.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, Markey Center for Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A, B, C, D
903Enterobacteria phage RB69Mutation(s): 2 
Gene Names: 43
EC: 2.7.7.7, 3.1.11.-
Find proteins for Q38087 (Enterobacteria phage RB69)
Go to UniProtKB:  Q38087
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'E,G,I,K18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3'F,H,J,L15N/A
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CTG
Query on CTG
E, G, I, K
DNA LINKINGC10 H17 N2 O10 PDT
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 132.612α = 90.00
b = 122.632β = 96.31
c = 168.695γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
Blu-Icedata collection
CNSphasing
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description