6U6B

Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink with Manganese in the active site

Summary for 6U6B

• Entry DOI: 10.2210/pdb6u6b/pdb
• Related: 6U2O
• Descriptor: DNA polymerase beta, DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3'), DNA (5'-D(P*GP*GP*TP*GP*AP*TP*GP*GP*GP*C)-3'), ... (9 entities in total)
• Functional Keywords: polymerase, cisplatin, mismatch, pt-gg, transferase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 48653.97

Authors

Ouzon-Shubeita, H.,Vilas, C.K.,Lee, S. (deposition date: 2019-08-29, release date: 2020-09-09, Last modification date: 2023-10-11)

Primary citation

Ouzon-Shubeita, H.,Vilas, C.K.,Lee, S.
Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion.
Biochem.J., 477:937-951, 2020

PubMed Abstract: The cisplatin-1,2-d(GpG) (Pt-GG) intrastrand cross-link is the predominant DNA lesion generated by cisplatin. Cisplatin has been shown to predominantly induce G to T mutations and Pt-GG permits significant misincorporation of dATP by human DNA polymerase β (polβ). In agreement, polβ overexpression, which is frequently observed in cancer cells, is linked to cisplatin resistance and a mutator phenotype. However, the structural basis for the misincorporation of dATP opposite Pt-GG is unknown. Here, we report the first structures of a DNA polymerase inaccurately bypassing Pt-GG. We solved two structures of polβ misincorporating dATP opposite the 5'-dG of Pt-GG in the presence of Mg2+ or Mn2+. The Mg2+-bound structure exhibits a sub-optimal conformation for catalysis, while the Mn2+-bound structure is in a catalytically more favorable semi-closed conformation. In both structures, dATP does not form a coplanar base pairing with Pt-GG. In the polβ active site, the syn-dATP opposite Pt-GG appears to be stabilized by protein templating and pi stacking interactions, which resembles the polβ-mediated dATP incorporation opposite an abasic site. Overall, our results suggest that the templating Pt-GG in the polβ active site behaves like an abasic site, promoting the insertion of dATP in a non-instructional manner.

PubMed: 32039434
DOI: 10.1042/BCJ20190906

Experimental method

X-RAY DIFFRACTION (3.108 Å)