PDBsum entry 3in5

Transferase/DNA

PDB id: 3in5

Contents

Protein chain

438 a.a. *

DNA/RNA

Ligands

ATP ×2

Metals

_MG ×4

Waters ×18

* Residue conservation analysis

PDB id:

3in5

Name:

Transferase/DNA

Title:

Structure of human DNA polymerase kappa inserting datp opposite an 8- oxog DNA lesion

Structure:

DNA polymerase kappa. Chain: a, b. Fragment: unp residues 19-526. Synonym: dinb protein, dinp. Engineered: yes. DNA (5'-d( Gp G Gp Gp Gp Ap Ap Gp Gp Ap Cp Tp (Doc))-3'). Chain: p, q. Engineered: yes. Other_details: DNA primer strand.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dinb1, polk. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Synthetic: yes. Synthetic: yes

Resolution:

3.20Å R-factor: 0.227 R-free: 0.274

Authors:

T.D.Silverstein,R.Vasquez-Del Carpio,A.K.Aggarwal

Key ref:

R.Vasquez-Del Carpio et al. (2009). Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion. Plos One, 4, e5766. PubMed id: 19492058

Date:

11-Aug-09 Release date: 08-Sep-09

Supersedes:

3hed

Protein chains

Q9UBT6  (POLK_HUMAN) -  DNA polymerase kappa from Homo sapiens

Seq: 870 a.a.

Struc: 438 a.a.

DNA/RNA chains

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

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

G-G-G-G-A-A-G-G-A-C-T-DOC 12 bases

A-8OG-G-A-G-T-C-C-T-T-C-C-C-C 14 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

Plos One 4:e5766 (2009)

PubMed id: 19492058

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

R.Vasquez-Del Carpio, T.D.Silverstein, S.Lone, M.K.Swan, J.R.Choudhury, R.E.Johnson, S.Prakash, L.Prakash, A.K.Aggarwal.

ABSTRACT

BACKGROUND: 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. METHODOLOGY AND PRINCIPAL FINDINGS: We show that the Polkappa active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP. CONCLUSIONS AND SIGNIFICANCE: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polkappa is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polkappa is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.