› 2w7p

X-ray diffraction
3.71Å resolution

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

Released:
DOI: 10.2210/pdb2w7p/pdb
PDB entry 2w7p coloured by chain, front view.
PDB entry 2w7p coloured by chain, side view.
PDB entry 2w7p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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 RL, Guengerich FP, Egli M
J Biol Chem 284 22467-22480 (2009)
PMID: 19542228

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-115898 (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: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UBT6 (Residues: 19-526; Coverage: 58%)
Gene names: DINB1, POLK
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3' Chains: E, P
Molecule details ›
Chains: E, P
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3' Chains: F, T
Molecule details ›
Chains: F, T
Length: 18 nucleotides
Theoretical weight: 5.39 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 2 x DTP
Ligand CA 4 x CA
1 modified residue:
Ligand 8OG 2 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 167.829Å b: 220.847Å c: 119.208Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.236 0.273
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine.
Beard et al. (2010)
4 more

6 mentions without citation

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