2DPJ

structure of hPoli with DNA and dTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota.

Nair, D.T.Johnson, R.E.Prakash, L.Prakash, S.Aggarwal, A.K.

(2006) Nat Struct Mol Biol 13: 619-625

  • DOI: 10.1038/nsmb1118
  • Primary Citation of Related Structures:  
    2DPJ, 2DPI

  • PubMed Abstract: 
  • The 1,N6-ethenodeoxyadenosine (epsilon dA) lesion is promutagenic and has been implicated in carcinogenesis. We show here that human Pol iota, a Y-family DNA polymerase, can promote replication through this lesion by proficiently incorporating a nucl ...

    The 1,N6-ethenodeoxyadenosine (epsilon dA) lesion is promutagenic and has been implicated in carcinogenesis. We show here that human Pol iota, a Y-family DNA polymerase, can promote replication through this lesion by proficiently incorporating a nucleotide opposite it. The structural basis of this action is rotation of the epsilon dA adduct to the syn conformation in the Pol iota active site and presentation of its 'Hoogsteen edge' for hydrogen-bonding with incoming dTTP or dCTP. We also show that Pol zeta carries out the subsequent extension reaction and that efficiency of extension from epsilon dA x T is notably higher than from epsilon dA x C. Together, our studies reveal for the first time how the exocyclic epsilon dA adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Pol iota and Pol zeta provides for efficient and error-free synthesis through this potentially carcinogenic DNA lesion.


    Organizational Affiliation

    Department of Molecular Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York 10029, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
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: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'P7N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'T9N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      TTP
      Query on TTP

      Download Ideal Coordinates CCD File 
      A
      THYMIDINE-5'-TRIPHOSPHATE
      C10 H17 N2 O14 P3
      NHVNXKFIZYSCEB-XLPZGREQSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.30 Å
      • R-Value Free: 0.277 
      • R-Value Work: 0.238 
      • R-Value Observed: 0.241 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.059α = 90
      b = 98.059β = 90
      c = 203.102γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      ADSCdata collection
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2006-07-04
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Advisory, Version format compliance