Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion

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.

Download Full-text

Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase β

Journal of Biological Chemistry ◽

10.1074/jbc.m114.605451 ◽

2014 ◽

Vol 289 (45) ◽

pp. 31341-31348 ◽

Cited By ~ 7

Author(s):

Myong-Chul Koag ◽

Lara Lai ◽

Seongmin Lee

Keyword(s):

Dna Polymerase ◽

Structural Basis ◽

Dna Polymerase Β ◽

Dna Lesion ◽

Human Dna ◽

Nucleotide Incorporation

Download Full-text

Structural basis for highly promutagenic replication across O6‐methylguanine by human DNA polymerase β (551.3)

The FASEB Journal ◽

10.1096/fasebj.28.1_supplement.551.3 ◽

2014 ◽

Vol 28 (S1) ◽

Author(s):

Seongmin Lee ◽

Myong‐Chul Koag ◽

Kyungjin Min

Keyword(s):

Dna Polymerase ◽

Structural Basis ◽

Dna Polymerase Β ◽

Human Dna

Download Full-text

Preferential Incorporation of G Opposite Template T by the Low-Fidelity Human DNA Polymerase ι

Molecular and Cellular Biology ◽

10.1128/mcb.20.19.7099-7108.2000 ◽

2000 ◽

Vol 20 (19) ◽

pp. 7099-7108 ◽

Cited By ~ 137

Author(s):

Yanbin Zhang ◽

Fenghua Yuan ◽

Xiaohua Wu ◽

Zhigang Wang

Keyword(s):

Dna Synthesis ◽

Dna Polymerase ◽

Polymerase Activity ◽

Abasic Site ◽

Base Pairing ◽

Base Pairs ◽

Dna Lesion ◽

Biological Source ◽

Human Dna ◽

Base Selection

ABSTRACT DNA polymerase activity is essential for replication, recombination, repair, and mutagenesis. All DNA polymerases studied so far from any biological source synthesize DNA by the Watson-Crick base-pairing rule, incorporating A, G, C, and T opposite the templates T, C, G, and A, respectively. Non-Watson-Crick base pairs would lead to mutations. In this report, we describe the ninth human DNA polymerase, Polι, encoded by the RAD30B gene. We show that human Polι violates the Watson-Crick base-pairing rule opposite template T. During base selection, human Polι preferred T-G base pairing, leading to G incorporation opposite template T. The resulting T-G base pair was less efficiently extended by human Polι compared to the Watson-Crick base pairs. Consequently, DNA synthesis frequently aborted opposite template T, a property we designated the T stop. This T stop restricted human Polι to a very short stretch of DNA synthesis. Furthermore, kinetic analyses show that human Polι copies template C with extraordinarily low fidelity, misincorporating T, A, and C with unprecedented frequencies of 1/9, 1/10, and 1/11, respectively. Human Polι incorporated one nucleotide opposite a template abasic site more efficiently than opposite a template T, suggesting a role for human Polι in DNA lesion bypass. The unique features of preferential G incorporation opposite template T and T stop suggest that DNA Polι may additionally play a specialized function in human biology.

Download Full-text

Covalent Trapping of Human DNA Polymerase β by the Oxidative DNA Lesion 2-Deoxyribonolactone

Journal of Biological Chemistry ◽

10.1074/jbc.c100577200 ◽

2002 ◽

Vol 277 (10) ◽

pp. 7637-7640 ◽

Cited By ~ 75

Author(s):

Michael S. DeMott ◽

Ergin Beyret ◽

Donny Wong ◽

Brian C. Bales ◽

Jae-Taeg Hwang ◽

...

Keyword(s):

Dna Polymerase ◽

Dna Polymerase Β ◽

Dna Lesion ◽

Human Dna ◽

Covalent Trapping

Download Full-text

Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase

Nature Communications ◽

10.1038/s41467-021-24317-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Olga Rechkoblit ◽

Robert E. Johnson ◽

Yogesh K. Gupta ◽

Louise Prakash ◽

Satya Prakash ◽

...

Keyword(s):

Dna Synthesis ◽

Dna Polymerase ◽

Thermodynamic Stability ◽

Active Site ◽

Base Pair ◽

Translesion Synthesis ◽

Human Cells ◽

Structural Basis ◽

Human Dna ◽

Dna Template

AbstractPrimPol is a human DNA polymerase-primase that localizes to mitochondria and nucleus and bypasses the major oxidative lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis, in mostly error-free manner. We present structures of PrimPol insertion complexes with a DNA template-primer and correct dCTP or erroneous dATP opposite the lesion, as well as extension complexes with C or A as a 3′−terminal primer base. We show that during the insertion of C and extension from it, the active site is unperturbed, reflecting the readiness of PrimPol to accommodate oxoG(anti). The misinsertion of A opposite oxoG(syn) also does not alter the active site, and is likely less favorable due to lower thermodynamic stability of the oxoG(syn)•A base-pair. During the extension step, oxoG(syn) induces an opening of its base-pair with A or misalignment of the 3′-A primer terminus. Together, the structures show how PrimPol accurately synthesizes DNA opposite oxidatively damaged DNA in human cells.

Download Full-text