4FS2

Base pairing mechanism of N2,3-ethenoguanine with dCTP by human polymerase iota


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases.

Zhao, L.Pence, M.G.Christov, P.P.Wawrzak, Z.Choi, J.Y.Rizzo, C.J.Egli, M.Guengerich, F.P.

(2012) J.Biol.Chem. 287: 35516-35526

  • DOI: 10.1074/jbc.M112.403253
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N(2),3-Ethenoguanine (N(2),3-εG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g. lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies ex ...

    N(2),3-Ethenoguanine (N(2),3-εG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g. lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies exploring the miscoding potential of this lesion are quite indirect because of the lability of the glycosidic bond. We utilized a 2'-fluoro isostere approach to stabilize this lesion and synthesized oligonucleotides containing 2'-fluoro-N(2),3-ε-2'-deoxyarabinoguanosine to investigate the miscoding potential of N(2),3-εG by Y-family human DNA polymerases (pols). In primer extension assays, pol η and pol κ replicated through N(2),3-εG, whereas pol ι and REV1 yielded only 1-base incorporation. Steady-state kinetics revealed that dCTP incorporation is preferred opposite N(2),3-εG with relative efficiencies in the order of pol κ > REV1 > pol η ≈ pol ι, and dTTP misincorporation is the major miscoding event by all four Y-family human DNA pols. Pol ι had the highest dTTP misincorporation frequency (0.71) followed by pol η (0.63). REV1 misincorporated dTTP and dGTP with much lower frequencies. Crystal structures of pol ι with N(2),3-εG paired to dCTP and dTTP revealed Hoogsteen-like base pairing mechanisms. Two hydrogen bonds were observed in the N(2),3-εG:dCTP base pair, whereas only one appears to be present in the case of the N(2),3-εG:dTTP pair. Base pairing mechanisms derived from the crystal structures explain the slightly favored dCTP insertion for pol ι in steady-state kinetic analysis. Taken together, these results provide a basis for the mutagenic potential of N(2),3-εG.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase iota
A
420Homo sapiensMutation(s): 0 
Gene 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: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*(EFG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')B,C18synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DCP
Query on DCP

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

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
EFG
Query on EFG
B, C
NON-POLYMERC12 H13 F N5 O7 PDG
DOC
Query on DOC
B, C
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.298α = 90.00
b = 97.298β = 90.00
c = 202.906γ = 120.00
Software Package:
Software NamePurpose
EMBLdata collection
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-06-26 
  • Released Date: 2012-08-29 
  • Deposition Author(s): Zhao, L.

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-09-12
    Type: Database references
  • Version 1.2: 2012-10-31
    Type: Database references