title: Structural basis for uracil recognition by archaeal family B DNA polymerases.
abstract: Deamination of cytosine to uracil in a G-C base pair is a major promutagenic event, generating G-C-->A-T mutations if not repaired before DNA replication. Archaeal family B DNA polymerases are uniquely able to recognize unrepaired uracil in a template strand and stall polymerization upstream of the lesion, thereby preventing the irreversible fixation of an A-T mutation. We have now identified a 'pocket' in the N-terminal domains of archaeal DNA polymerases that is positioned to interact with the template strand and provide this ability. The structure of this pocket provides interacting groups that discriminate uracil from the four normal DNA bases (including thymine). These groups are conserved in archaeal polymerases but absent from homologous viral polymerases that are unable to recognize uracil. Using site-directed mutagenesis, we have confirmed the biological role of this pocket and have engineered specific mutations in the Pfu polymerase that confer the ability to read through template-strand uracils and carry out PCR with dUTP in place of dTTP.
authors.affiliation: School of Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Fogg
authors.forename: Laurence H
authors.initials: LH
authors.lastname: Pearl
authors.forename: Bernard A
authors.initials: BA
authors.lastname: Connolly
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology*; D001665:Binding Sites; D017124:Conserved Sequence; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013045:Species Specificity; D014498:Uracil / Q000737:chemistry* / Q000378:metabolism; D014780:Viruses / Q000201:enzymology
chemical_list: D014498:Uracil; D004259:DNA-Directed DNA Polymerase