ddCTP:G pair in the polymerase active site (0 position)

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

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This is version 2.1 of the entry. See complete history


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 U S A 103: 19701-19706

  • DOI: https://doi.org/10.1073/pnas.0609580103
  • Primary Citation of Related Structures:  
    2HHQ, 2HHS, 2HHT, 2HHU, 2HHV, 2HHW, 2HHX, 2HVH, 2HVI, 2HW3

  • 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 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA Polymerase IE [auth A],
F [auth D]
580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KWC1 
Go to UniProtKB:  Q5KWC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KWC1
Sequence Annotations
  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'A [auth B],
C [auth E]
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'B [auth C],
D [auth F]
Sequence Annotations
  • Reference Sequence


Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
G, H
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.795α = 90
b = 108.492β = 90
c = 149.403γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary