Solution Structure of a Trans-Opened (10S)-dA Adduct of (+)-(7S,8R,9S,10R)-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a Fully Complementary DNA Duplex:  Evidence for a Major Syn Conformation

Pradhan, Padmanava; Tirumala, Sampath; Liu, Xiaohong; Sayer, Jane M.; Jerina, Donald M.; Yeh, Herman J. C.

doi:10.1021/bi002896q

Cited by 43 publications

(46 citation statements)

References 51 publications

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“…The simple interpretation of these data is that BPdA inhibition of transesterification is a consequence of disruption of contacts between the topoisomerase and the base pairs of the CCCTT target site that are critical to trigger DNA cleavage. This view is consistent with NMR data showing that single R and S BPdA adducts cause spreading and buckling of the base pairs immediately flanking the intercalated BP moiety (32)(33)(34)(35)(36) (Fig. 2).…”

Section: Discussionsupporting

confidence: 90%

“…This difference is noteworthy given that the ϩ2R adduct (which intercalates from the major groove on the 5Ј side of the ϩ2A) and the ϩ1S adduct (which intercalates on the 3Ј side of the ϩ1A) are both insinuated between the ϩ2 T:A and ϩ1 T:A base pairs. We presume that subtle differences in space occupancy by the intercalated ring systems or their induced DNA distortions (32)(33)(34)(35)(36)54) are responsible for the different effects of the ϩ2R and ϩ1S BPdA adducts on topoisomerase cleavage.…”

Section: Discussionmentioning

confidence: 99%

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Site-specific DNA Transesterification by Vaccinia Topoisomerase

Yakovleva

Tian

Sayer

et al. 2003

Journal of Biological Chemistry

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Vaccinia DNA topoisomerase forms a covalent DNA-(3-phosphotyrosyl)-enzyme intermediate at a specific target site 5-C ؉5 C ؉4 C ؉3 T ؉2 T ؉1 p2N ؊1 in duplex DNA. Here we study the effects of base modifications on the rate and extent of single-turnover DNA transesterification. Chiral trans opened C-10 R and S adducts of benzo[a]pyrene (BP) 7,8-diol 9,10-epoxide were introduced at single N 6 -deoxyadenosine (dA) positions within the 3-sequence of the nonscissile DNA strand. The R and S BPdA adducts intercalate from the major groove on the 5 and 3 sides of the modified base, respectively, and perturb local base stacking. We found that R and S BPdA modifications at ؉1A reduced the transesterification rate by a factor of 700 -1000 without affecting the yield of the covalent topoisomerase-DNA complex. BPdA modifications at ؉2A reduced the extent of transesterification and elicited rate decrements of 200-and 7000-fold for the S and R diastereomers, respectively. In contrast, BPdA adducts at the ؊2 position had no effect on the extent of the reaction and relatively little impact on the rate of cleavage. A more subtle probe of major groove contacts entailed substituting each of the purines of the nonscissile strand with its 8-oxo analog. The ؉3 oxoG modification slowed transesterification 35-fold, whereas other 8-oxo modifications were benign. 8-Oxo substitutions at the ؊1 position in the scissile strand slowed single-turnover cleavage by a factor of six but had an even greater slowing effect on religation, which resulted in an increase in the cleavage equilibrium constant. 2-Aminopurine at positions ؉3, ؉4, or ؉5 in the nonscissile strand had no effect on transesterification per se but had synergistic effects when combined with 8-oxoA at position ؊1 in the scissile strand. These findings illuminate the functional interface of vaccinia topoisomerase with the DNA major groove.Poxvirus DNA topoisomerase is an attractive target for drug therapy of smallpox in light of its unique DNA recognition specificity, compact structure, and distinctive pharmacological sensitivities compared with human topoisomerase I (1-6). Poxvirus topoisomerase, exemplified by the 314-amino acid vaccinia virus enzyme, is a prototype of the type IB DNA topoisomerase family (7-9). Type IB enzymes cleave and rejoin one strand of the DNA duplex through a transient DNA-(3Ј-phosphotyrosyl)-enzyme intermediate.Poxvirus topoisomerases bind and cleave duplex DNA at a pentapyrimidine target sequence, 5Ј-(T/C)CCTTp2 (3). The T2 nucleotide (defined as the ϩ1 nucleotide) is linked to Tyr-274 of the vaccinia enzyme. Four conserved amino acid side chains found in all type IB topoisomerases (Arg-130, Lys-167, Arg-223, and His-265 in the vaccinia enzyme) are responsible for catalyzing the attack by tyrosine on the scissile phosphodiester to form the covalent intermediate (10 -12). The topoisomerase binds to DNA as a C-shaped protein clamp formed by an 80-amino acid N-terminal domain that contacts the DNA major groove and a 234-amino acid C-terminal catalytic domain ...

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Site-specific DNA Transesterification by Vaccinia Topoisomerase

Yakovleva

Tian

Sayer

et al. 2003

Journal of Biological Chemistry

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“…3A) and higher temperature factors. Structural characterization of BPDE-dA adducts by NMR to date has found the hydrocarbon intercalated only between base pairs and not in the major groove (5,6,24). To accommodate the PAH in the major groove without clashing with the neighboring base pairs, the dA* slides toward the major groove by nearly 2 Å (Fig.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of a benzo[ a ]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase

Sayer

Plosky

et al. 2004

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

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The first occupation-associated cancers to be recognized were the sooty warts (cancers of the scrotum) suffered by chimney sweeps in 18th century England. In the 19th century, high incidences of skin cancers were noted among fuel industry workers. By the early 20th century, malignant skin tumors were produced in laboratory animals by repeatedly painting them with coal tar. The culprit in coal tar that induces cancer was finally isolated in 1933 and determined to be benzo[a]pyrene (BP), a polycyclic aromatic hydrocarbon. A residue of fuel and tobacco combustion and frequently ingested by humans, BP is metabolized in mammals to benzo[a]pyrene diol epoxide (BPDE), which forms covalent DNA adducts and induces tumor growth. In the 70 yr since its isolation, BP has been the most studied carcinogen. Yet, there has been no crystal structure of a BPDE DNA adduct. We report here the crystal structure of a BPDE-adenine adduct base-paired with thymine at a templateprimer junction and complexed with the lesion-bypass DNA polymerase Dpo4 and an incoming nucleotide. Two conformations of the BPDE, one intercalated between base pairs and another solvent-exposed in the major groove, are observed. The latter conformation, which can be stabilized by organic solvents that reduce the dielectric constant, seems more favorable for DNA replication by Dpo4. These structures also suggest a mechanism by which mutations are generated during replication of DNA containing BPDE adducts.

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“…The structural features of bulky lesions derived from the binding of (ϩ)-or (Ϫ)-anti-BPDE to N 2 -dG or N 6 -dA (Scheme 1) have been extensively studied (37)(38)(39). Such lesions are strong blocks of DNA replication catalyzed by a variety of classical replicative DNA polymerases in vitro, but inefficient mutagenic bypass is often observed (22, 24, 26 -28, 40).…”

mentioning

confidence: 99%

“…Subtle stereochemical differences in the adducts can give rise to marked differences in their mutagenic properties in cellular environments (41)(42)(43). The stereochemical characteristics of the lesions, as well as the modified purine nucleobase, exert a profound influence on the conformational characteristics of the adducts in DNA (37)(38)(39)44). It is therefore of significant interest to compare and determine how such stereochemically and structurally well defined stereoisomeric [BP]-N 2 -dG (G*) and [BP]-N 6 -dA (A*) lesions affect trans-lesion bypass catalyzed by purified polymerases pol (hDinB1), pol (hRad30A), pol (hRad30B), and yeast pol (Rev3 and Rev7) in vitro.…”

mentioning

confidence: 99%

trans-Lesion Synthesis Past Bulky Benzo[a]pyrene Diol Epoxide N2-dG and N6-dA Lesions Catalyzed by DNA Bypass Polymerases

Rechkoblit

Zhang

Guo

et al. 2002

Journal of Biological Chemistry

186

181

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The effectiveness of in vitro primer elongation reactions catalyzed by human bypass DNA polymerases (hDinB1), pol (hRad30A), pol (hRad30B), and yeast pol (Rev3 and Rev7) in site-specifically modified template oligonucleotide strands were studied in vitro. The templates contained single bulky lesions derived from the trans-addition of the mutagenic (؉)-or (؊)-enantiomers of r7,t8-dihydroxy-t9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (a metabolite of the environmental carcinogen benzo[a]pyrene), to the exocyclic amino groups of guanine or adenine in oligonucleotide templates 33, or more, bases long. In "running start" primer extension reactions, pol effectively bypassed both the stereoisomeric (؉)-and (؊)-trans-guanine adducts but not the analogous adenine adducts. In sharp contrast, pol , which exhibits considerable sequence homology with pol (both belong to the group of Y family polymerases), is partially blocked by the guanine adducts and the (؊)-trans-adenine adduct, although the stereoisomeric (؉)-trans-adenine adduct is more successfully bypassed. Neither pol nor pol , either alone or in combination, were effective in trans-lesion synthesis past the same adducts. In all cases, the fidelity of insertion is dependent on adduct stereochemistry and structure. Generally, error-free nucleotide insertion opposite the lesions tends to depend more on adduct stereochemistry than error-prone insertion. None of the polymerases tested are a universal bypass polymerase for the stereoisomeric bulky polycyclic aromatic hydrocarbon-DNA adducts derived from anti-BPDE.Several new prokaryotic and eukaryotic DNA polymerases (pol) 1 involved in trans-lesional synthesis have been recently identified (reviewed in Refs. 1-5). The functional characteristics of the UmuC/DinB/Rev1p/Rad30 DNA polymerases belonging to the Y family of DNA polymerases (5) have been extensively investigated (6 -11). These polymerases are able to bypass a variety of DNA lesions in vitro (8,(12)(13)(14)(15)(16)(17)(18)(19)(20) that are known to block replication catalyzed by "classical" polymerases such as pol ␣, pol ␤, phage T7, the Klenow fragment of pol I from Escherichia coli, and human immunodeficiency virusreverse transcriptase, etc. (see Refs. 21-18 for example).The efficiencies and fidelities of trans-lesion synthesis catalyzed by Y family polymerases vary significantly among the different subfamilies and also depend remarkably on the type of DNA damage. Purified human pol (DinB1, 870 amino acids in size) efficiently bypasses (Ϫ)-trans-[BP]-N 2 -dG adducts (bulky lesions derived from the binding of the mutagen r7,t8-dihydroxy-t9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene ((ϩ)-or (Ϫ)-anti-BPDE) to the exocyclic amino groups of guanine and adenine residues in DNA (Scheme 1) with the insertion of a C opposite the lesion (12). A truncated form of pol , a 560-amino acid form pol (⌬C), missing motifs VIIa and VIIb and obtained from a baculovirus expression system, also bypasses the (ϩ)- trans-[BP]-N2 -dG adduct (29). Human pol also bypasses 8-oxo-dG lesio...

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Solution Structure of a Trans-Opened (10S)-dA Adduct of (+)-(7S,8R,9S,10R)-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a Fully Complementary DNA Duplex: Evidence for a Major Syn Conformation

Cited by 43 publications

References 51 publications

Site-specific DNA Transesterification by Vaccinia Topoisomerase

Site-specific DNA Transesterification by Vaccinia Topoisomerase

Crystal structure of a benzo[ a ]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase

trans-Lesion Synthesis Past Bulky Benzo[a]pyrene Diol Epoxide N2-dG and N6-dA Lesions Catalyzed by DNA Bypass Polymerases

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