3IN5

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase kappa
A, B
508Homo sapiensMutation(s): 0 
Gene Names: POLK (DINB1)
EC: 2.7.7.7
Find proteins for Q9UBT6 (Homo sapiens)
Go to Gene View: POLK
Go to UniProtKB:  Q9UBT6
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3')P,Q13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')T,U18N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
T, U
DNA LINKINGC10 H14 N5 O8 PDG
DOC
Query on DOC
P, Q
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 116.846α = 90.00
b = 154.480β = 90.00
c = 217.293γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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