PDBsum entry 3gil

Transferase/DNA

PDB id: 3gil

Contents

Protein chains

341 a.a. *

DNA/RNA

Ligands

DGT ×2

Metals

_CA ×6

Waters ×119

* Residue conservation analysis

PDB id:

3gil

Name:

Transferase/DNA

Title:

Dpo4 extension ternary complex with oxog(anti)-t(anti) pair

Structure:

DNA polymerase iv. Chain: a, b. Synonym: pol iv. Engineered: yes. 5'-d( Gp Tp Tp Gp Gp Ap Tp Gp Gp Tp Ap Gp (2Dt))-3'. Chain: d, h. Engineered: yes. Other_details: primer strand (dideoxy-terminated at 3'-end). 5'-d( Cp Tp Ap Ap Cp (8Og)

Source:

Sulfolobus solfataricus p2. Organism_taxid: 273057. Strain: p2 / dsm 1617 / jcm 11322. Atcc: 35092. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: DNA primer strand.

Resolution:

2.71Å R-factor: 0.203 R-free: 0.259

Authors:

O.Rechkoblit,L.Malinina,D.J.Patel

Key ref:

O.Rechkoblit et al. (2009). Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Structure, 17, 725-736. PubMed id: 19446528

Date:

05-Mar-09 Release date: 19-May-09

Protein chains

Q97W02  (DPO4_SULSO) -  DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 352 a.a.

Struc: 341 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-T-T-G-G-A-T-G-G-T-A-G-2DT 13 bases

C-T-A-A-C-8OG-C-T-A-C-C-A-T-C-C-A-A-C 18 bases

G-T-T-G-G-A-T-G-G-T-A-G-2DT 13 bases

A-A-C-8OG-C-T-A-C-C-A-T-C-C-A-A-C 16 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

Structure 17:725-736 (2009)

PubMed id: 19446528

Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.

O.Rechkoblit, L.Malinina, Y.Cheng, N.E.Geacintov, S.Broyde, D.J.Patel.

ABSTRACT

7,8-Dihydro-8-oxoguanine (oxoG), the predominant oxidative DNA damage lesion, is processed differently by high-fidelity and Y-family lesion bypass polymerases. Although high-fidelity polymerases extend predominantly from an A base opposite an oxoG, the Y-family polymerases Dpo4 and human Pol eta preferentially extend from the oxoG*C base pair. We have determined crystal structures of extension Dpo4 ternary complexes with oxoG opposite C, A, G, or T and the next nascent base pair. We demonstrate that neither template backbone nor the architecture of the active site is perturbed by the oxoG(anti)*C and oxoG*A pairs. However, the latter manifest conformational heterogeneity, adopting both oxoG(syn)*A(anti) and oxoG(anti)*A(syn) alignment. Hence, the observed reduced primer extension from the dynamically flexible 3'-terminal primer base A is explained. Because of homology between Dpo4 and Pol eta, such a dynamic screening mechanism might be utilized by Dpo4 and Pol eta to regulate error-free versus error-prone bypass of oxoG and other lesions.