PDBsum entry 3epg

Transferase/DNA

PDB id: 3epg

Contents

Protein chain

375 a.a. *

DNA/RNA

Ligands

DCP

Metals

_NA ×4

Waters ×69

* Residue conservation analysis

PDB id:

3epg

Name:

Transferase/DNA

Title:

Structure of human DNA polymerase iota complexed with n2-ethylguanine

Structure:

DNA polymerase iota. Chain: a. Fragment: catalytic fragment (unp residues 1-420). Synonym: rad30 homolog b, eta2. Engineered: yes. 5'-d( Dtp Dcp Dtp (2Eg) p Dgp Dgp Dgp Dtp Dcp Dcp Dtp Dap Dgp Dgp Dap Dcp Dcp (Doc))-3'. Chain: b, c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: poli, poli (amino acids 1-420), rad30b. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: a self-annealing oligonucletoide was synthesized by midland certified reagents containing n2-ethylgaunine using

Resolution:

2.50Å R-factor: 0.237 R-free: 0.283

Authors:

M.G.Pence

Key ref:

M.G.Pence et al. (2009). Lesion bypass of N2-ethylguanine by human DNA polymerase iota. J Biol Chem, 284, 1732-1740. PubMed id: 18984581 DOI: 10.1074/jbc.M807296200

Date:

29-Sep-08 Release date: 16-Dec-08

Protein chain

Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota from Homo sapiens

Seq: 740 a.a.

Struc: 375 a.a.

DNA/RNA chains

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

2EG-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.M807296200

J Biol Chem 284:1732-1740 (2009)

PubMed id: 18984581

Lesion bypass of N2-ethylguanine by human DNA polymerase iota.

M.G.Pence, P.Blans, C.N.Zink, T.Hollis, J.C.Fishbein, F.W.Perrino.

ABSTRACT

Nucleotide incorporation and extension opposite N2-ethyl-Gua by DNA polymerase iota was measured and structures of the DNA polymerase iota-N2-ethyl-Gua complex with incoming nucleotides were solved. Efficiency and fidelity of DNA polymerase iota opposite N2-ethyl-Gua was determined by steady state kinetic analysis with Mg2+ or Mn2+ as the activating metal. DNA polymerase iota incorporates dCMP opposite N2-ethyl-Gua and unadducted Gua with similar efficiencies in the presence of Mg2+ and with greater efficiencies in the presence of Mn2+. However, the fidelity of nucleotide incorporation by DNA polymerase iota opposite N2-ethyl-Gua and Gua using Mn2+ is lower relative to that using Mg2+ indicating a metal-dependent effect. DNA polymerase iota extends from the N2-ethyl-Gua:Cyt 3' terminus more efficiently than from the Gua:Cyt base pair. Together these kinetic data indicate that the DNA polymerase iota catalyzed reaction is well suited for N(2)-ethyl-Gua bypass. The structure of DNA polymerase iota with N2-ethyl-Gua at the active site reveals the adducted base in the syn configuration when the correct incoming nucleotide is present. Positioning of the ethyl adduct into the major groove removes potential steric overlap between the adducted template base and the incoming dCTP. Comparing structures of DNA polymerase iota complexed with N2-ethyl-Gua and Gua at the active site suggests movements in the DNA polymerase iota polymerase-associated domain to accommodate the adduct providing direct evidence that DNA polymerase iota efficiently replicates past a minor groove DNA adduct by positioning the adducted base in the syn configuration.

Selected figure(s)

Figure 2.
The structures of DNA pol ι·N^2-ethyl-Gua Complexes with incoming dCTP or dTTP. A, the structure of DNA pol ι containing N^2-ethyl-Gua and incoming dCTP shows the N^2-ethyl-Gua base rotated into the syn configuration. B, the structure of DNA pol ι containing N^2-ethyl-Gua and incoming dTTP shows the N^2-ethyl-Gua base in the anti configuration and the N^2-adduct protruding into the minor groove. C, electron density around the N^2-ethyl adduct and incoming dCTP. D, electron density around the N^2-ethyl adduct and the γ phosphate of the incoming dTTP.

Figure 4.
Repositioning of Lys^309 in the structure of DNA pol ι with N^2-ethyl-Gua in the syn configuration. A, the Lys^309 side chain in DNA pol ι in complex with N^2-ethyl-Gua (green) in the syn configuration shifts ∼9Å relative to the position of Lys^309 in DNA pol ι complexed with syn Gua (PDB code 2ALZ, magenta). B, with N^2-ethyl-Gua in the anti conformation (blue) Lys^309 remains in a similar position relative to the Lys^309 in the DNA pol ι·Gua complex (PDB code 2FLP, yellow).

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2009, 284, 1732-1740) copyright 2009.

Figures were selected by an automated process.