4EYH

Human DNA polymerase iota incorporating dCTP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase.

Kirouac, K.N.Basu, A.K.Ling, H.

(2013) Nucleic Acids Res. 41: 2060-2071

  • DOI: 10.1093/nar/gks1296
  • Primary Citation of Related Structures:  4EYI

  • PubMed Abstract: 
  • Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in e ...

    Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyrene-derived DNA lesions generates mutations that likely play a role in the etiology of cancer. Here, we report two crystal structures of the human Y-family DNA polymerase iota complexed with the major 1-nitropyrene DNA lesion at the insertion stage, incorporating either dCTP or dATP nucleotide opposite the lesion. PolĪ¹ maintains the adduct in its active site in two distinct conformations. dCTP forms a Watson-Crick base pair with the adducted guanine and excludes the pyrene ring from the helical DNA, which inhibits replication beyond the lesion. By contrast, the mismatched dATP stacks above the pyrene ring that is intercalated in the helix and achieves a productive conformation for misincorporation. The intra-helical bulky pyrene mimics a base pair in the active site and facilitates adenine misincorporation. By structure-based mutagenesis, we show that the restrictive active site of human polĪ· prevents the intra-helical conformation and A-base misinsertions. This work provides one of the molecular mechanisms for G to T transversions, a signature mutation in human lung cancer.


    Organizational Affiliation

    Department of Biochemistry, Medical Sciences Building 334, University of Western Ontario, London, ON N6A 5C1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase iota
B
420Homo sapiensGene Names: POLI (RAD30B)
EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens)
Go to Gene View: POLI
Go to UniProtKB:  Q9UNA4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA templateT8N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA primerP7N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

Download SDF File 
Download CCD File 
B
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DG8
Query on DG8
T
DNA LINKINGC26 H23 N6 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.239 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.046α = 90.00
b = 98.046β = 90.00
c = 194.649γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
ADSCdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-05-01 
  • Released Date: 2013-01-09 
  • Deposition Author(s): Kirouac, K., Ling, H.

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references