› 3in5

X-ray diffraction
3.2Å resolution

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

Released:
DOI: 10.2210/pdb3in5/pdb
PDB entry 3in5 coloured by chain, front view.
PDB entry 3in5 coloured by chain, side view.
PDB entry 3in5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion.
Vasquez-Del Carpio R, Silverstein TD, Lone S, Swan MK, Choudhury JR, Johnson RE, Prakash S, Prakash L, Aggarwal AK
PLoS One 4 e5766 (2009)
PMID: 19492058

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116415 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase kappa Chains: A, B
Molecule details ›
Chains: A, B
Length: 508 amino acids
Theoretical weight: 58.04 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q9UBT6 (Residues: 19-526; Coverage: 58%)
Gene names: DINB1, POLK
Sequence domains:
Structure domains:
DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*(DOC))-3') Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*C*CP*TP*AP*(8OG)P*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chains: T, U
Molecule details ›
Chains: T, U
Length: 18 nucleotides
Theoretical weight: 5.4 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ATP 2 x ATP
Ligand MG 4 x MG
2 modified residues:
Ligand DOC 2 x DOC
Ligand 8OG 2 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: C2221
Unit cell:
a: 116.846Å b: 154.48Å c: 217.293Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.225 0.274
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

5 review citations

DNA glycosylase encoded by MUTYH functions as a molecular switch for programmed cell death under oxidative stress to suppress tumorigenesis.
Oka et al. (2011)
4 more

9 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
8 more