3EPI

Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine and incoming TTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

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:  
    3EPG, 3EPI

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase iotaA420Homo sapiensMutation(s): 0 
Gene Names: POLIRAD30B
EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens)
Explore Q9UNA4 
Go to UniProtKB:  Q9UNA4
NIH Common Fund Data Resources
PHAROS  Q9UNA4
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    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
    PO4
    Query on PO4

    Download Ideal Coordinates CCD File 
    A
    PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    A
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.90 Å
    • R-Value Free: 0.282 
    • R-Value Work: 0.236 
    • R-Value Observed: 0.239 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 98.643α = 90
    b = 98.643β = 90
    c = 202.231γ = 120
    Software Package:
    Software NamePurpose
    CrystalCleardata collection
    PHASERphasing
    REFMACrefinement
    d*TREKdata reduction
    d*TREKdata scaling

    Structure Validation

    View Full Validation Report



    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
      Changes: Advisory, Version format compliance