PDBsum entry 2w7o

DNA binding protein

PDB id: 2w7o

Contents

Protein chain

432 a.a. *

DNA/RNA

Ligands

DGT ×2

Metals

_CA ×4

Waters ×30

* Residue conservation analysis

PDB id:

2w7o

Name:

DNA binding protein

Title:

Structure and activity of bypass synthesis by human DNA polymerase kappa opposite the 7,8-dihydro-8-oxodeoxyguanosine adduct

Structure:

DNA polymerase kappa. Chain: a, b. Fragment: residues 19-526. Synonym: dinb, dinp. Engineered: yes. Other_details: human DNA polymerase kappa catalytic core, residues 19-526. 5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Tp Tp C)-3'. Chain: e, p.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polk, dinb1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Resolution:

3.16Å R-factor: 0.241 R-free: 0.278

Authors:

A.Irimia,M.Egli

Key ref:

A.Irimia et al. (2009). 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. J Biol Chem, 284, 22467-22480. PubMed id: 19542228

Date:

23-Dec-08 Release date: 16-Jun-09

Protein chains

Q9UBT6  (POLK_HUMAN) -  DNA polymerase kappa from Homo sapiens

Seq: 870 a.a.

Struc: 432 a.a.

DNA/RNA chains

G-G-G-A-A-G-G-A-T-T-C 11 bases

C-A-C-8OG-G-A-A-T-C-C-T-T-C-C-C 15 bases

G-G-G-G-G-A-A-G-G-A-T-T-C 13 bases

C-A-C-8OG-G-A-A-T-C-C-T-T-C-C-C-C-C 17 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

J Biol Chem 284:22467-22480 (2009)

PubMed id: 19542228

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.

A.Irimia, R.L.Eoff, F.P.Guengerich, M.Egli.

ABSTRACT

Human polymerase kappa (hPol kappa) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress. Here, we present a detailed analysis of the activity and specificity of hPol kappa bypass opposite the major oxidative adduct 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG). Unlike its archaeal homolog Dpo4, hPol kappa bypasses this lesion in an error-prone fashion by inserting mainly dATP. Analysis of transient-state kinetics shows diminished "bursts" for dATP:8-oxoG and dCTP:8-oxoG incorporation, indicative of non-productive complex formation, but dATP:8-oxoG insertion events that do occur are 2-fold more efficient than dCTP:G insertion events. Crystal structures of ternary hPol kappa complexes with adducted template-primer DNA reveal non-productive (dGTP and dATP) alignments of incoming nucleotide and 8-oxoG. Structural limitations placed upon the hPol kappa by interactions between the N-clasp and finger domains combined with stabilization of the syn-oriented template 8-oxoG through the side chain of Met-135 both appear to contribute to error-prone bypass. Mutating Leu-508 in the little finger domain of hPol kappa to lysine modulates the insertion opposite 8-oxoG toward more accurate bypass, similar to previous findings with Dpo4. Our structural and activity data provide insight into important mechanistic aspects of error-prone bypass of 8-oxoG by hPol kappa compared with accurate and efficient bypass of the lesion by Dpo4 and polymerase eta.