3M9N

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

Summary for 3M9N

• Entry DOI: 10.2210/pdb3m9n/pdb
• Related: 3M9M 3M9O
• Descriptor: DNA polymerase IV, DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*GP*C)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), ... (7 entities in total)
• Functional Keywords: dpo4, translesion dna synthesis, tls, cisplatin, y-family dna polymerase, protein-dna complex, dna, dna damage, dna repair, dna replication, dna-binding, dna-directed dna polymerase, magnesium, metal-binding, mutator protein, nucleotidyltransferase, transferase, transferase-dna complex, transferase/dna
• Biological source: Sulfolobus solfataricus; More
• Cellular location: Cytoplasm : Q97W02
• Total number of polymer chains: 3
• Total formula weight: 50621.45

Authors

Wong, J.H.Y.,Ling, H. (deposition date: 2010-03-22, release date: 2010-06-16, Last modification date: 2024-03-13)

Primary citation

Wong, J.H.,Brown, J.A.,Suo, Z.,Blum, P.,Nohmi, T.,Ling, H.
Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4.
Embo J., 29:2059-2069, 2010

PubMed 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.

PubMed: 20512114
DOI: 10.1038/emboj.2010.101

Experimental method

X-RAY DIFFRACTION (1.93 Å)