2HHW

ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structural basis for the mutagenicity of O6-methyl-guanine lesions.

Warren, J.J.Forsberg, L.J.Beese, L.S.

(2006) Proc.Natl.Acad.Sci.Usa 103: 19701-19706

  • DOI: 10.1073/pnas.0609580103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methylating agents are widespread environmental carcinogens that generate a broad spectrum of DNA damage. Methylation at the guanine O(6) position confers the greatest mutagenic and carcinogenic potential. DNA polymerases insert cytosine and thymine ...

    Methylating agents are widespread environmental carcinogens that generate a broad spectrum of DNA damage. Methylation at the guanine O(6) position confers the greatest mutagenic and carcinogenic potential. DNA polymerases insert cytosine and thymine with similar efficiency opposite O(6)-methyl-guanine (O6MeG). We combined pre-steady-state kinetic analysis and a series of nine x-ray crystal structures to contrast the reaction pathways of accurate and mutagenic replication of O6MeG in a high-fidelity DNA polymerase from Bacillus stearothermophilus. Polymerases achieve substrate specificity by selecting for nucleotides with shape and hydrogen-bonding patterns that complement a canonical DNA template. Our structures reveal that both thymine and cytosine O6MeG base pairs evade proofreading by mimicking the essential molecular features of canonical substrates. The steric mimicry depends on stabilization of a rare cytosine tautomer in C.O6MeG-polymerase complexes. An unusual electrostatic interaction between O-methyl protons and a thymine carbonyl oxygen helps stabilize T.O6MeG pairs bound to DNA polymerase. Because DNA methylators constitute an important class of chemotherapeutic agents, the molecular mechanisms of replication of these DNA lesions are important for our understanding of both the genesis and treatment of cancer.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA Polymerase I
A, D
580Geobacillus kaustophilus (strain HTA426)Mutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5KWC1
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'E,B9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'F,C13N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

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A, D
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
MN
Query on MN

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A, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
23T
Query on 23T

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A, D
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DDG
Query on DDG
B, E
DNA LINKINGC10 H14 N5 O6 PDG
6OG
Query on 6OG
C, F
DNA LINKINGC11 H16 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.834α = 90.00
b = 108.897β = 90.00
c = 150.111γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description