Efficient and High Fidelity Incorporation of dCTP Opposite 7,8-Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

Hong, Zhou; Irimia, A.; Choi, Jeong‐Yun; Angel, Karen C.; Loukachevitch, Lioudmila V.; Egli, Martin; Guengerich, F. Peter

doi:10.1074/jbc.m510889200

Cited by 118 publications

(150 citation statements)

References 59 publications

(79 reference statements)

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“…To allow for the stabilization of 8-oxoG in the anti-conformation and to promote correct dCTP incorporation opposite the lesion, the 5Ј-phosphate group must be shifted to avoid a steric clash with the O8 atom on the modified base. The outward motion of the LF domain therefore likely acts to pull the damaged template base and phosphate into this distorted configuration via interactions between the O8 and phosphate oxygen atoms on the DNA and the LF domain residues Arg-331 and Arg-332 (15,17). Our steady-state fluorescence data indicate that this outward motion of the LF domain is larger than the changes observed in the other domains (supplemental Table S3), which underlines the importance of this conformational change.…”

Section: Discussioncontrasting

confidence: 38%

“…Based on crystallographic evidence, there is a large interface of the LF domain that interacts with the DNA substrate. Moreover, the loop between ␤-sheets 2 and 3 of the finger domain interacts with ␤-sheet 9 of the LF domain, which is in direct contact with the DNA template strand (15,17). Thus, the dynamics of the finger domain may be influenced by those of the LF domain.…”

Section: Discussionmentioning

confidence: 99%

“…Crystallographic evidence suggests that Dpo4 makes several additional contacts with a DNA substrate containing an 8-oxoG lesion, which are not possible with an undamaged DNA substrate (15)(16)(17). Thus, although studies have shown that Dpo4 can bypass 8-oxoG and unmodified DNA bases with similar efficiency (17), it is possible that these additional interactions are able to perturb the conformational dynamics of Dpo4 during nucleotide incorporation in the vicinity of the damaged base. Here, this hypothesis was examined through transient kinetic and dynamic studies of the bypass of an 8-oxoG lesion and the subsequent extension catalyzed by Dpo4.…”

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confidence: 96%

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DNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis

Maxwell

Suo

2012

Journal of Biological Chemistry

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Background: Y-family DNA polymerases may employ protein conformational changes to catalyze the bypass of various DNA lesions. Results: The conformational dynamics of three structural domains of Dpo4 are altered by 8-oxo-7,8-dihydro-2Ј-deoxyguanine (8-oxoG). Conclusion: Dpo4 undergoes different global conformational changes during 8-oxoG bypass than during the replication of undamaged DNA. Significance: A DNA lesion alters the conformational dynamics of a DNA polymerase during catalysis.

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Section: Discussioncontrasting

confidence: 38%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 96%

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DNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis

Maxwell

Suo

2012

Journal of Biological Chemistry

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“…4A). Such mutagenic base pairing has been observed for Bacillus fragment (BF pol I) and T7 polymerase (T7) from the high-fidelity A family (4,5), polβ from the X family (26,27), and polκ and Dpo4 from the Y family (2,28) (Fig. 4A).…”

Section: Resultsmentioning

confidence: 99%

Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota

Kirouac

2011

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

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The 8-oxo-guanine (8-oxo-G) lesion is the most abundant and mutagenic oxidative DNA damage existing in the genome. Due to its dual coding nature, 8-oxo-G causes most DNA polymerases to misincorporate adenine. Human Y-family DNA polymerase iota (polι) preferentially incorporates the correct cytosine nucleotide opposite 8-oxo-G. This unique specificity may contribute to polι's biological role in cellular protection against oxidative stress. However, the structural basis of this preferential cytosine incorporation is currently unknown. Here we present four crystal structures of polι in complex with DNA containing an 8-oxo-G lesion, paired with correct dCTP or incorrect dATP, dGTP, and dTTP nucleotides. An exceptionally narrow polι active site restricts the purine bases in a syn conformation, which prevents the dual coding properties of 8-oxo-G by inhibiting syn/anti conformational equilibrium. More importantly, the 8-oxo-G base in a syn conformation is not mutagenic in polι because its Hoogsteen edge does not form a stable base pair with dATP in the narrow active site. Instead, the syn 8-oxo-G template base forms the most stable replicating base pair with correct dCTP due to its small pyrimidine base size and enhanced hydrogen bonding with the Hoogsteen edge of 8-oxo-G. In combination with site directed mutagenesis, we show that Gln59 in the finger domain specifically interacts with the additional O 8 atom of the lesion base, which influences nucleotide selection, enzymatic efficiency, and replication stalling at the lesion site. Our work provides the structural mechanism of high-fidelity 8-oxo-G replication by a human DNA polymerase.DNA replication | Y family polymerase | translesion DNA synthesis | oxidative lesion | DNA mutagenesis

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“…Likewise, X-ray crystallographic structures of Dpo4 in complex with DNA, both with and without dNTP have been determined (for example, see Refs [4,[13][14][15][16][17]). Crystal structures of lesion-containing complexes for these two polymerases are also available (for example, see Refs [14,[18][19][20][21][22][23][24][25][26][27]), which shed light on their contrasting mechanisms for processing damaged DNA templates. We consider two important DNA lesion prototypes as examples of small and bulky lesions, respectively: 7,8-dihydro-8-oxoguanine (8-oxoG; Box 2), a ubiquitous product of reactive oxygen species (ROS), and DNA adducts derived from a tumorigenic metabolite of the environmental pre-carcinogen benzo[a]pyrene (BP; Box 3).…”

mentioning

confidence: 99%

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

Broyde¹,

Wang²,

Rechkoblit³

et al. 2008

Trends in Biochemical Sciences

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When a high-fidelity DNA polymerase encounters certain DNA-damage sites, its progress can be stalled and one or more lesion-bypass polymerases are recruited to transit the lesion. Here, we consider two representative types of lesions: (i) 7,8-dihydro-8-oxogua-nine (8-oxoG), a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo [a]pyrene, in the high-fidelity DNA polymerase Bacillus fragment (BF) from Bacillus stearothermophilus and in the lesion-bypass DNA polymerase IV (Dpo4) from Sulfolobus solfataricus. The tight fit of the BF polymerase around the nascent base pair contrasts with the more spacious, solvent-exposed active site of Dpo4, and these differences in architecture result in distinctions in their respective functions: one-step versus stepwise polymerase translocation, mutagenic versus accurate bypass of 8-oxoG, and polymerase stalling versus mutagenic bypass at bulky benzo[a]pyrene-derived lesions. Lesions and DNA polymerasesUntil 1999, it was widely understood that bacteria have three DNA polymerases and mammals have five [1]. In 1999, however, an entirely new category of polymerases was discovered in prokaryotes and eukaryotes [2-4] -the lesion-bypass DNA polymerases. The function of lesion-bypass polymerases is to replicate past lesion-containing DNA templates in a process called translesion synthesis [5][6][7]. Now at least 16 DNA polymerases are known in eukaryotes [8] and five in bacteria [9]. Furthermore, since 1999, crystal structures of DNA polymerases, including those containing lesions, have provided new structural insights into the mechanistic aspects of translesion synthesis and polymerase stalling associated with DNA lesions. For a review of the structures and mechanisms of DNA polymerases up to the year 2005, see Ref.[10].Here, we discuss the structural and functional features of representative high-fidelity and lesion-bypass DNA polymerases (Box 1) and how these features affect the processing of certain forms of DNA damage. The lesions considered are derived from reactions of intermediates produced by endogenous sources or from the metabolic activation of environmental genotoxic

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Efficient and High Fidelity Incorporation of dCTP Opposite 7,8-Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

Cited by 118 publications

References 59 publications

DNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis

DNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis

Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

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