Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion

Batra, V.K.; Shock, David D.; Beard, William A.; McKenna, Charles E.; Wilson, Samuel H.

doi:10.1073/pnas.1112235108

Cited by 69 publications

(165 citation statements)

References 44 publications

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“…In addition, an ordered water molecule stabilizes syn-BrG by bridging BrG and Tyr-271. The preferred syn conformation of BrG in the templating base position is in contrast with the previous observation that oxoG in the same position exists as a mixture of syn and anti conformers (14,18), suggesting that size of C8-substituent may govern base conformation in the templating base position. The presence of synBrG in DNA triggers a local conformational change at the template DNA, where the BrG lesion moved ϳ10 Å away from the position of G nucleotide residue seen in the published binary complex structure (PDB ID 1BPX) (19).…”

Section: Structure Of a Single-nucleotide Gapped Binary Complex Ofcontrasting

confidence: 99%

“…8, C and E). The similar conformational reorganization of templating base and its phosphate backbone has been observed in pol␤ ternary structure with Hoogsteen syn-oxoG⅐dATP or Watson-Crick anti-oxoG⅐dCTP base pair (14,18).…”

Section: Discussionsupporting

confidence: 64%

“…They were purified by the manufacturer, and their sequences were confirmed by MALDI-TOF mass spectrometry. DNA substrates used for crystallographic studies consisted of a 16-mer template, a complementary 10-mer primer, and 5-mer downstream oligonucleotides (18). The template DNA sequence used for crystallization was 5Ј-CCGAC[BrG]TCGCATCAGC-3Ј.…”

Section: Methodsmentioning

confidence: 99%

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Structural Basis for Promutagenicity of 8-Halogenated Guanine

Koag

Min

Lee

2014

Journal of Biological Chemistry

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Background: 8-Halogenated guanine is a promutagenic lesion that promotes insertion of guanine opposite the lesion during DNA replication. Results: 8-Bromoguanine forms Hoogsteen base pairing with G and Watson-Crick base pairing with C in the active site of pol␤. Conclusion: 8-Bromoguanine is well accommodated in the nascent base pair binding pocket of pol␤. Significance: Our structural studies provide insights into potential G to C mutations.

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Section: Structure Of a Single-nucleotide Gapped Binary Complex Ofcontrasting

confidence: 99%

Section: Discussionsupporting

confidence: 64%

Section: Methodsmentioning

confidence: 99%

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Structural Basis for Promutagenicity of 8-Halogenated Guanine

Koag

Min

Lee

2014

Journal of Biological Chemistry

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“…The 5Cl atom is 3.9 and 4.3 Å away from the backbone phosphate oxygen atoms (Fig. 4B) and is accommodated within the major groove of the DNA, in contrast to other known mutagenic lesions, such as 8oxoG, which occupies both the syn-and anti-conformations in the open binary complex because of the steric clash of the O8 with the phosphate backbone (35).…”

Section: Results 5clc Is a Mutagenic Base That Is Easily Bypassed By mentioning

confidence: 99%

Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer

Fedeles

Freudenthal

Yau

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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During chronic inflammation, neutrophil-secreted hypochlorous acid can damage nearby cells inducing the genomic accumulation of 5-chlorocytosine (5ClC), a known inflammation biomarker. Although 5ClC has been shown to promote epigenetic changes, it has been unknown heretofore if 5ClC directly perpetrates a mutagenic outcome within the cell. The present work shows that 5ClC is intrinsically mutagenic, both in vitro and, at a level of a single molecule per cell, in vivo. Using biochemical and genetic approaches, we have quantified the mutagenic and toxic properties of 5ClC, showing that this lesion caused C→T transitions at frequencies ranging from 3-9% depending on the polymerase traversing the lesion. X-ray crystallographic studies provided a molecular basis for the mutagenicity of 5ClC; a snapshot of human polymerase β replicating across a primed 5ClC-containing template uncovered 5ClC engaged in a nascent base pair with an incoming dATP analog. Accommodation of the chlorine substituent in the template major groove enabled a unique interaction between 5ClC and the incoming dATP, which would facilitate mutagenic lesion bypass. The type of mutation induced by 5ClC, the C→T transition, has been previously shown to occur in substantial amounts both in tissues under inflammatory stress and in the genomes of many inflammation-associated cancers. In fact, many sequence-specific mutational signatures uncovered in sequenced cancer genomes feature C→T mutations. Therefore, the mutagenic ability of 5ClC documented in the present study may constitute a direct functional link between chronic inflammation and the genetic changes that enable and promote malignant transformation.5-chloro-deoxycytidine | hypochlorite | myeloperoxidase | inflammatory bowel disease | carcinogenesis

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“…This compound has a high mutagenic potential due to its ability to preferably interact with adenine instead of cytosine [16]. The presence of 8odG in the template DNA strand can lead to binding of dATP opposite to it in the active center of DNA polymerase with the subsequent replacement dC → dA in the growing chain (strand) [2,16,41] (one should mention that binding of dCTP opposite to the template 8odG is possible too). The 8odG in the composition of the incoming nucleotide triphosphate (8oxoGTP, fig.…”

Section: Introductionmentioning

confidence: 99%

Features of the 8-oxo-7,8-dihydro-2′-dGTP behavior in active site of human DNA polymerase β: structural investigation in silico

Nyporko

2014

Biol. Stud.

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The oxidized bases in the composition of DNA as well as DNA precursors (desoxynucleotide triphosphates, dNTPs) appearing in living cell as a result of oxidative stress are the one of major sources of genomic instability. Among oxidized forms of nitrogenous bases, the 8-oxo-7,8-dihydro-2-deoxyguanine (8odG, 8-oxo-dG) is the most ubiquitous. This compound has a high mutagenic potential due to its ability to preferably interact with adenine instead of cytosine. In particular, the 8odG in the composition of the incoming nucleotide triphosphate (8-oxo-GTP) is able to immediately incorporate into the growing DNA chain and, thus, to cause the invert replacement dA → dC because it is possible to pair with the incoming dCTP as well as dATP in the next round of DNA replication.The efficiency of 8oxo-dG incorporation in growing DNA clearly depends on the nature of appropriate DNA polymerases. One of the most sensitive to 8-oxo-dGTP is the eukaryotic DNA polymerase β (pol β). The binding of 8-oxo-dGTP in the active center of pol β can result in two different molecular events. First of them is the incorporation of 8oxoguanine into a growing DNA chain, the other is a discrimination of 8-oxo-dGTP from the active center. While effects of incorporation of this modified guanine in DNA are well studied, the immediate consequences of 8-oxo-dGTP discrimination are still unclear.The behavior of 8-oxo-dGTP molecule in the area of the active site of human DNA polymerase β was investigated using molecular dynamics (MD) calculation. The principle phenomenon revealed as investigation results is existence of two cardinally different models of behavior inherent to 8-oxo-dGTP molecule. In two cases the ligand molecules loses the connections with template dA and starts to migrate inside of enzyme space (migrate trajectories). In the other two cases 8-oxo-dGTP stably stays in DNA polymerase active site, "keeps in touch" with template nucleotide and maintains the hydrogen bonds with it (stable trajectories).The spatial structure of 8-oxo-dGTP in stable trajectories appears to be sufficiently rigid despite the presence of number of bonds around which the free rotation is possible, and its conformational energy is characterized by high stability over the time of studied MD. Average values of energy (-10229.7 and -10227.1 kJ/mol) are practically the same for both cases. Amino acid microenvironment of 8-oxo-dGTP also practically doesn't change over the studied MD interval. Thus, stable variants of 8-oxo-dGTP behavior evidently correspond to case of the further incorporation modified 8-oxo-dG into growing DNA strand. The behavior of 8-oxo-dGTP molecule in migrate trajectories is significantly more complicated. The 8-oxo-dGTP loses the Н-bonds with template dA6 (at 11 and 6.5 ns of MD in first and second case respectively) and starts to migrate in DNA polymerase space. The 8-oxo-dGTP spatial structure regularly exhibits much more flexibility in comparison to itself behavior in stable trajectories that reflects in corresponded values of individual ato...

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Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion

Cited by 69 publications

References 44 publications

Structural Basis for Promutagenicity of 8-Halogenated Guanine

Structural Basis for Promutagenicity of 8-Halogenated Guanine

Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer

Features of the 8-oxo-7,8-dihydro-2′-dGTP behavior in active site of human DNA polymerase β: structural investigation in silico

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