2W7O

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

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Literature

Structural and Functional Elucidation of the Mechanism Promoting Error-Prone Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine Adduct.

Irimia, A.Eoff, R.L.Guengerich, F.P.Egli, M.

(2009) J Biol Chem 284: 22467

  • DOI: 10.1074/jbc.M109.003905
  • Primary Citation of Related Structures:  
    2W7O, 2W7P

  • PubMed Abstract: 
  • Human polymerase kappa (hPol kappa) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress ...

    Human polymerase kappa (hPol kappa) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress. Here, we present a detailed analysis of the activity and specificity of hPol kappa bypass opposite the major oxidative adduct 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG). Unlike its archaeal homolog Dpo4, hPol kappa bypasses this lesion in an error-prone fashion by inserting mainly dATP. Analysis of transient-state kinetics shows diminished "bursts" for dATP:8-oxoG and dCTP:8-oxoG incorporation, indicative of non-productive complex formation, but dATP:8-oxoG insertion events that do occur are 2-fold more efficient than dCTP:G insertion events. Crystal structures of ternary hPol kappa complexes with adducted template-primer DNA reveal non-productive (dGTP and dATP) alignments of incoming nucleotide and 8-oxoG. Structural limitations placed upon the hPol kappa by interactions between the N-clasp and finger domains combined with stabilization of the syn-oriented template 8-oxoG through the side chain of Met-135 both appear to contribute to error-prone bypass. Mutating Leu-508 in the little finger domain of hPol kappa to lysine modulates the insertion opposite 8-oxoG toward more accurate bypass, similar to previous findings with Dpo4. Our structural and activity data provide insight into important mechanistic aspects of error-prone bypass of 8-oxoG by hPol kappa compared with accurate and efficient bypass of the lesion by Dpo4 and polymerase eta.


    Organizational Affiliation

    Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASE KAPPAA, B508Homo sapiensMutation(s): 0 
Gene Names: POLKDINB1
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT6 (Homo sapiens)
Explore Q9UBT6 
Go to UniProtKB:  Q9UBT6
PHAROS:  Q9UBT6
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'C [auth E], E [auth P]13N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3'D [auth F], F [auth T]18N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.16 Å
      • R-Value Free: 0.278 
      • R-Value Work: 0.241 
      • R-Value Observed: 0.241 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 165.482α = 90
      b = 217.629β = 90
      c = 117.957γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      • Deposited Date: 2008-12-23 
      • Released Date: 2009-06-16 
      • Deposition Author(s): Irimia, A., Egli, M.

      Revision History  (Full details and data files)

      • Version 1.0: 2009-06-16
        Type: Initial release
      • Version 1.1: 2011-05-08
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance