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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase kappa
A, B
508Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBT6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description