3L8B

Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin.

Aller, P.Ye, Y.Wallace, S.S.Burrows, C.J.Doublie, S.

(2010) Biochemistry 49: 2502-2509

  • DOI: https://doi.org/10.1021/bi902195p
  • Primary Citation of Related Structures:  
    3L8B

  • PubMed Abstract: 

    The oxidation of guanine generates one of the most common DNA lesions, 8-oxo-7,8-dihydroguanine (8-oxoG). The further oxidation of 8-oxoG can produce either guanidinohydantoin (Gh) in duplex DNA or spiroiminodihydantoin (Sp) in nucleosides and ssDNA. Although Gh can be a strong block for replicative DNA polymerases such as RB69 DNA polymerase, this lesion is also mutagenic: DNA polymerases bypass Gh by preferentially incorporating a purine with a slight preference for adenine, which results in G.C --> T.A or G.C --> C.G transversions. The 2.15 A crystal structure of the replicative RB69 DNA polymerase in complex with DNA containing Gh reveals that Gh is extrahelical and rotated toward the major groove. In this conformation Gh is no longer in position to serve as a templating base for the incorporation of an incoming nucleotide. This work also constitutes the first crystallographic structure of Gh, which is stabilized in the R configuration in the two polymerase/DNA complexes present in the crystal asymmetric unit. In contrast to 8-oxoG, Gh is found in a high syn conformation in the DNA duplex and therefore presents the same hydrogen bond donor and acceptor pattern as thymine, which explains the propensity of DNA polymerases to incorporate a purine opposite Gh when bypass occurs.


  • Organizational Affiliation

    Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, Vermont 05405, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase
A, B
906Escherichia phage RB69Mutation(s): 2 
Gene Names: 43gp43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38087
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
C, E
18N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3')
D, F
13N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.276α = 90
b = 120.246β = 95.96
c = 136.963γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description