PDBsum entry 3m9m

Transferase/DNA

PDB id: 3m9m

Contents

Protein chain

341 a.a. *

DNA/RNA

Ligands

CTP

GOL ×3

CPT

Metals

_CA ×4

Waters ×51

* Residue conservation analysis

PDB id:

3m9m

Name:

Transferase/DNA

Title:

Crystal structure of dpo4 in complex with DNA containing the major cisplatin lesion

Structure:

DNA polymerase iv. Chain: b. Synonym: pol iv. Engineered: yes. DNA (5'-d( Gp Gp Gp Gp Gp Ap Ap Gp Gp Ap Ap Ap G)-3'). Chain: p. Engineered: yes. DNA (5'- d( Tp Cp Tp Gp Gp Cp Tp Tp Tp Cp Cp Tp Tp Cp Cp Cp Cp C)-3').

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Strain: p2. Gene: dbh, dpo4, sso2448. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.90Å R-factor: 0.285 R-free: 0.309

Authors:

J.H.Y.Wong,H.Ling

Key ref:

J.H.Wong et al. (2010). Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4. Embo J, 29, 2059-2069. PubMed id: 20512114

Date:

22-Mar-10 Release date: 16-Jun-10

Protein chain

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.

DNA/RNA chains

G-G-G-G-G-A-A-G-G-A-A-A-G 13 bases

G-G-C-T-T-T-C-C-T-T-C-C-C-C-C 15 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

Embo J 29:2059-2069 (2010)

PubMed id: 20512114

Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4.

J.H.Wong, J.A.Brown, Z.Suo, P.Blum, T.Nohmi, H.Ling.

ABSTRACT

Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG DNA. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3'G (first insertion) and 5'G (second insertion) of Pt-GG, and the primer extension beyond the lesion site. We observed a dynamic process, in which the lesion was converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4. The DNA translocation-coupled conformational change may account for additional inhibition on the second insertion reaction. The structures illustrate that Pt-GG disturbs the replicating base pair in the active site, which reduces the catalytic efficiency and fidelity. The in vivo relevance of Dpo4-mediated Pt-GG bypass was addressed by a dpo-4 knockout strain of Sulfolobus solfataricus, which exhibits enhanced sensitivity to cisplatin and proteomic alterations consistent with genomic stress.