3M9M: Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion

Citation:
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.
PDB ID: 3M9MDownload
MMDB ID: 82825
PDB Deposition Date: 2010/3/22
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.9  Å
Source Organism:
Sulfolobus solfataricus
Similar Structures:
Biological Unit for 3M9M: trimeric; determined by author and by software (PISA)
Molecular Components in 3M9M
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase IV(Gene symbol: SSO_RS11880)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*gp*gp*gp*gp*gp*ap*ap*gp*gp*ap*ap*ap*g)-3')
Molecule annotation
1
DNA (5'-d(*tp*cp*tp*gp*gp*cp*tp*tp*tp*cp*cp*tp*tp*cp*cp*cp*cp*c)-3')
Molecule annotation
Chemicals (9 molecules)
1
1
2
4
3
3
4
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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