title: Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.
abstract: One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg(2+) appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.
authors.affiliation: †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States.
authors.forename: Rajan
authors.initials: R
authors.lastname: Vyas
authors.affiliation: †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Reed
authors.affiliation: †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States.
authors.forename: E John
authors.initials: EJ
authors.lastname: Tokarsky
authors.affiliation: †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States.
authors.forename: Zucai
authors.initials: Z
authors.lastname: Suo
mesh_terms: D000080242:8-Hydroxy-2'-Deoxyguanosine / Q000031:analogs & derivatives; D055162:Biocatalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004249:DNA Damage; D019951:DNA Polymerase beta / Q000737:chemistry* / Q000378:metabolism*; D011756:Diphosphates / Q000737:chemistry / Q000378:metabolism; D006147:Guanine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008670:Metals / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011487:Protein Conformation; D013997:Time Factors
chemical_list: D011756:Diphosphates; D008670:Metals; D006147:Guanine; C078307:8-oxo-7,8-dihydrodeoxyguanine; D000080242:8-Hydroxy-2'-Deoxyguanosine; D019951:DNA Polymerase beta
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