3EPG

Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lesion bypass of N2-ethylguanine by human DNA polymerase iota.

Pence, M.G.Blans, P.Zink, C.N.Hollis, T.Fishbein, J.C.Perrino, F.W.

(2009) J.Biol.Chem. 284: 1732-1740

  • DOI: 10.1074/jbc.M807296200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleotide incorporation and extension opposite N2-ethyl-Gua by DNA polymerase iota was measured and structures of the DNA polymerase iota-N2-ethyl-Gua complex with incoming nucleotides were solved. Efficiency and fidelity of DNA polymerase iota oppo ...

    Nucleotide incorporation and extension opposite N2-ethyl-Gua by DNA polymerase iota was measured and structures of the DNA polymerase iota-N2-ethyl-Gua complex with incoming nucleotides were solved. Efficiency and fidelity of DNA polymerase iota opposite N2-ethyl-Gua was determined by steady state kinetic analysis with Mg2+ or Mn2+ as the activating metal. DNA polymerase iota incorporates dCMP opposite N2-ethyl-Gua and unadducted Gua with similar efficiencies in the presence of Mg2+ and with greater efficiencies in the presence of Mn2+. However, the fidelity of nucleotide incorporation by DNA polymerase iota opposite N2-ethyl-Gua and Gua using Mn2+ is lower relative to that using Mg2+ indicating a metal-dependent effect. DNA polymerase iota extends from the N2-ethyl-Gua:Cyt 3' terminus more efficiently than from the Gua:Cyt base pair. Together these kinetic data indicate that the DNA polymerase iota catalyzed reaction is well suited for N(2)-ethyl-Gua bypass. The structure of DNA polymerase iota with N2-ethyl-Gua at the active site reveals the adducted base in the syn configuration when the correct incoming nucleotide is present. Positioning of the ethyl adduct into the major groove removes potential steric overlap between the adducted template base and the incoming dCTP. Comparing structures of DNA polymerase iota complexed with N2-ethyl-Gua and Gua at the active site suggests movements in the DNA polymerase iota polymerase-associated domain to accommodate the adduct providing direct evidence that DNA polymerase iota efficiently replicates past a minor groove DNA adduct by positioning the adducted base in the syn configuration.


    Organizational Affiliation

    Department of Biochemistry and Center for Structural Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
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: 2
MoleculeChainsLengthOrganism
5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'B,C18N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Download SDF File 
Download CCD File 
A
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
2EG
Query on 2EG
B, C
DNA LINKINGC12 H18 N5 O7 PG
DOC
Query on DOC
B, C
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.535α = 90.00
b = 98.535β = 90.00
c = 202.354γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
CrystalCleardata collection
d*TREKdata reduction
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-09-29 
  • Released Date: 2008-12-16 
  • Deposition Author(s): Pence, M.G.

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance