PDBsum entry 3osn

Transferase/DNA

PDB id: 3osn

Contents

Protein chain

385 a.a. *

DNA/RNA

Ligands

TTP

Metals

_MG ×2

_NA

Waters ×271

* Residue conservation analysis

PDB id:

3osn

Name:

Transferase/DNA

Title:

Structural basis for proficient incorporation of dttp opposite o6- methylguanine by human DNA polymerase iota

Structure:

5'-d( Tp Cp Tp (6Og) p Gp Gp Gp Tp Cp Cp Tp Ap Gp Gp Ap Cp Cp (Doc))-3'. Chain: b, c. Engineered: yes. DNA polymerase iota. Chain: a. Fragment: catalytic fragment, residues 1-420. Synonym: eta2, rad30 homolog b. Engineered: yes

Source:

Synthetic: yes. Other_details: the oligonucleotide was synthesized by midland certified reagent company inc.. Homo sapiens. Human. Organism_taxid: 9606. Gene: poli, rad30b. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.210 R-free: 0.241

Authors:

M.G.Pence

Key ref:

M.G.Pence et al. (2010). Structural basis for proficient incorporation of dTTP opposite O6-methylguanine by human DNA polymerase iota. J Biol Chem, 285, 40666-40672. PubMed id: 20961860 DOI: 10.1074/jbc.M110.183665

Date:

09-Sep-10 Release date: 20-Oct-10

Protein chain

Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota from Homo sapiens

Seq: 740 a.a.

Struc: 385 a.a.

DNA/RNA chains

A-G-G-A-C-C-DOC 7 bases

6OG-G-G-G-T-C-C-T 8 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

DOI no: 10.1074/jbc.M110.183665

J Biol Chem 285:40666-40672 (2010)

PubMed id: 20961860

Structural basis for proficient incorporation of dTTP opposite O6-methylguanine by human DNA polymerase iota.

M.G.Pence, J.Y.Choi, M.Egli, F.P.Guengerich.

ABSTRACT

O(6)-methylguanine (O(6)-methylG) is highly mutagenic and is commonly found in DNA exposed to methylating agents, even physiological ones (e.g. S-adenosylmethionine). The efficiency of a truncated, catalytic DNA polymerase ι core enzyme was determined for nucleoside triphosphate incorporation opposite O(6)-methylG, using steady-state kinetic analyses. The results presented here corroborate previous work from this laboratory using full-length pol ι, which showed that dTTP incorporation occurs with high efficiency opposite O(6)-methylG. Misincorporation of dTTP opposite O(6)-methylG occurred with ∼6-fold higher efficiency than incorporation of dCTP. Crystal structures of the truncated form of pol ι with O(6)-methylG as the template base and incoming dCTP or dTTP were solved and showed that O(6)-methylG is rotated into the syn conformation in the pol ι active site and that dTTP misincorporation by pol ι is the result of Hoogsteen base pairing with the adduct. Both dCTP and dTTP base paired with the Hoogsteen edge of O(6)-methylG. A single, short hydrogen bond formed between the N3 atom of dTTP and the N7 atom of O(6)-methylG. Protonation of the N3 atom of dCTP and bifurcation of the N3 hydrogen between the N7 and O(6) atoms of O(6)-methylG allow base pairing of the lesion with dCTP. We conclude that differences in the Hoogsteen hydrogen bonding between nucleotides is the main factor in the preferential selectivity of dTTP opposite O(6)-methylG by human pol ι, in contrast to the mispairing modes observed previously for O(6)-methylG in the structures of the model DNA polymerases Sulfolobus solfataricus Dpo4 and Bacillus stearothermophilus DNA polymerase I.