3IN5

Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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Literature

Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion

Vasquez-Del Carpio, R., Silverstein, T.D., Lone, S., Swan, M.K., Choudhury, J.R., Johnson, R.E., Prakash, S., Prakash, L., Aggarwal, A.K.

(2009) PLoS One 4: e5766-e5766

  • DOI: 10.1371/journal.pone.0005766
  • Primary Citation of Related Structures:  
    3IN5

  • PubMed Abstract: 

    • Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C ...

    Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase kappa (Polkappa) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polkappa's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polkappa in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide.

    Organizational Affiliation: 

    Department of Structural & Chemical Biology, Mount Sinai School of Medicine, New York, NY, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase kappaA, B508Homo sapiensMutation(s): 0 
Gene Names: DINB1, POLK
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
GTEx:  ENSG00000122008
Protein Feature View
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  • Reference Sequence
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    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3')C [auth P], E [auth Q]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')D [auth T], F [auth U]18N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.20 Å
      • R-Value Free: 0.274 
      • R-Value Work: 0.225 
      • R-Value Observed: 0.227 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 116.846α = 90
      b = 154.48β = 90
      c = 217.293γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2009-09-08
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance