title: Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications.
abstract: Chemicals and radiation can damage DNA leading to the formation of adducts/lesions, which - if not removed by DNA repair pathways - usually block replicative DNA polymerases (DNAPs). To overcome such potentially lethal blockage, cells have lesion bypass DNAPs, which are often in the Y-Family and include several classes. One class includes human DNAP kappa and E. coli DNAP IV, and they insert dCTP in the non-mutagenic pathway opposite [+ta]-B[a]P-N(2)-dG, which is the major adduct formed by the environmental carcinogen benzo[a]pyrene. Another class includes hDNAP eta and ecDNAP V, and they insert dATP opposite [+ta]-B[a]P-N(2)-dG in the dominant G-->T mutagenic pathway. Herein we develop a hypothesis for why the IV/kappa-class preferentially does cellular dCTP insertion. On the minor groove side of the active site, Y-Family DNAPs have a cleft/hole that can be analyzed based on an analogy to a "chimney." Our models of DNAP IV show a large chimney opening from which the pyrene of [+ta]-B[a]P-N(2)-dG can protrude, which allows canonical adduct-dG:dCTP pairing. In contrast, our models of DNAP V have small chimney openings that forces adduct-dG downward in the active site such that canonical adduct-dG:dCTP pairing is not possible. Based on X-ray structures, sequence alignment and our modeled structures of Y-Family DNAPs, chimney opening size seems primarily controlled by one amino acid ("flue-handle"), which dictates whether nearby amino acids ("flue") plug the chimney or not. Based on this analysis, a correlation is apparent: the flue is closed in V/eta-class DNAPs giving small chimney openings, while the flue is open for the IV/kappa-class giving large chimney openings. Secondarily, a hypothesis is developed for why the V/eta-class might preferentially do cellular dATP insertion opposite [+ta]-B[a]P-N(2)-dG: the small chimney forces adduct-dG lower in the active site, possibly leading to catalysis using a non-canonical dNTP shape that permits syn-adenine:adduct-dG base pairing. In summary, a hypothesize is developed that the pyrene moiety of [+ta]-B[a]P-N(2)-dG protrudes from the large chimney opening of DNAP IV, thus permitting canonical dCTP:adduct-dG pairing, while the small chimney opening of DNAP V forces [+ta]-B[a]P-N(2)-dG lower down in the active site, in which syn-adenine can pair with adduct-dG via a non-canonical dNTP shape.
authors.affiliation: Biology Department, Boston University, Boston, MA 02215, USA.
authors.forename: Sushil
authors.initials: S
authors.lastname: Chandani
authors.forename: Edward L
authors.initials: EL
authors.lastname: Loechler
mesh_terms: D000595:Amino Acid Sequence; D001580:Benzopyrenes / Q000737:chemistry / Q000378:metabolism*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D018736:DNA Adducts / Q000378:metabolism*; D019951:DNA Polymerase beta / Q000378:metabolism; D004260:DNA Repair; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism*; D030562:Databases, Protein; D003838:Deoxyadenine Nucleotides / Q000378:metabolism; D003845:Deoxycytosine Nucleotides / Q000378:metabolism; D003849:Deoxyguanosine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D003854:Deoxyribonucleotides / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D005998:Glycine; D006801:Humans; D008957:Models, Genetic; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D000099270:Y-Family DNA Polymerases
chemical_list: D001580:Benzopyrenes; D018736:DNA Adducts; D019951:DNA Polymerase beta; D004259:DNA-Directed DNA Polymerase; D003838:Deoxyadenine Nucleotides; D003845:Deoxycytosine Nucleotides; D003849:Deoxyguanosine; D003854:Deoxyribonucleotides; D029968:Escherichia coli Proteins; D005998:Glycine; C478198:benzo(a)pyrene N2-dG adduct; C024107:2'-deoxycytidine 5'-triphosphate; C078202:UmuC protein, E coli; C509838:Dpo4 protein, E coli; C120926:DNA polymerase V, E coli; C404302:POLK protein, human; D000099270:Y-Family DNA Polymerases; C026600:2'-deoxyadenosine triphosphate