title: Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex.
abstract: Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 Å-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Shuangluo
authors.initials: S
authors.lastname: Xia
authors.forename: William H
authors.initials: WH
authors.lastname: Konigsberg
authors.forename: Jimin
authors.initials: J
authors.lastname: Wang
mesh_terms: D018360:Crystallography, X-Ray; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009154:Mutation; D017434:Protein Structure, Tertiary; D013942:Thymine Nucleotides / Q000737:chemistry*; D014050:Toluene / Q000031:analogs & derivatives* / Q000737:chemistry; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D013942:Thymine Nucleotides; D014764:Viral Proteins; D014050:Toluene; C110527:difluorotoluene; D004259:DNA-Directed DNA Polymerase; C463461:bacteriophage RB69 DNA polymerase; C024157:thymidine 5'-triphosphate