4B9L

Structure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA DNA lesion in the pre-insertion site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions.

Gehrke, T.H.Lischke, U.Gasteiger, K.L.Schneider, S.Arnold, S.Muller, H.C.Stephenson, D.S.Zipse, H.Carell, T.

(2013) Nat.Chem.Biol. 9: 455

  • DOI: 10.1038/nchembio.1254
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1' glycosidic bo ...

    8-Oxopurines (8-oxodG and 8-oxodA) and formamidopyrimidines (FaPydG and FaPydA) are major oxidative DNA lesions involved in cancer development and aging. Their mutagenicity is believed to result from a conformational shift of the N9-C1' glycosidic bonds from anti to syn, which allows the lesions to form noncanonical Hoogsteen-type base pairs with incoming triphosphates during DNA replication. Here we present biochemical data and what are to our knowledge the first crystal structures of carbocyclic FaPydA and FaPydG containing DNA in complex with a high-fidelity polymerase. Crystallographic snapshots show that the cFaPy lesions keep the anti geometry of the glycosidic bond during error-free and error-prone replication. The observed dG·dC→dT·dA transversion mutations are the result of base shifting and tautomerization.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department of Chemistry, Ludwig Maximilians University, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE I
A
619Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Go to UniProtKB:  E1C9K5
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'B10Geobacillus stearothermophilus
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'C15Geobacillus stearothermophilus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

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Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FAX
Query on FAX
C
DNA LINKINGC11 H18 N5 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.528α = 90.00
b = 93.265β = 90.00
c = 106.107γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references, Structure summary
  • Version 1.2: 2013-05-29
    Type: Database references
  • Version 1.3: 2013-07-03
    Type: Database references