title: Novel inhibition of archaeal family-D DNA polymerase by uracil.
abstract: Archaeal family-D DNA polymerase is inhibited by the presence of uracil in DNA template strands. When the enzyme encounters uracil, following three parameters change: DNA binding increases roughly 2-fold, the rate of polymerization slows by a factor of ≈ 5 and 3'-5' proof-reading exonuclease activity is stimulated by a factor of ≈ 2. Together these changes result in a significant decrease in polymerization activity and a reduction in net DNA synthesis. Pol D appears to interact with template strand uracil irrespective of its distance ahead of the replication fork. Polymerization does not stop at a defined location relative to uracil, rather a general decrease in DNA synthesis is observed. 'Trans' inhibition, the slowing of Pol D by uracil on a DNA strand not being replicated is also observed. It is proposed that Pol D is able to interact with uracil by looping out the single-stranded template, allowing simultaneous contact of both the base and the primer-template junction to give a polymerase-DNA complex with diminished extension ability.
authors: Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
authors: Tomas T
authors: TT
authors: Richardson
authors: Louise
authors: L
authors: Gilroy
authors: Yoshizumi
authors: Y
authors: Ishino
authors: Bernard A
authors: BA
authors: Connolly
authors: Ghislaine
authors: G
authors: Henneke
mesh_terms: D004247:DNA / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D003838:Deoxyadenine Nucleotides / Q000378:metabolism; D003854:Deoxyribonucleotides / Q000378:metabolism; D005092:Exonucleases / Q000378:metabolism; D019384:Nucleic Acid Synthesis Inhibitors; D019711:Pyrococcus / Q000201:enzymology*; D013698:Templates, Genetic; D014498:Uracil / Q000378:metabolism*
chemical_list: D004277:DNA, Single-Stranded; D003838:Deoxyadenine Nucleotides; D003854:Deoxyribonucleotides; D019384:Nucleic Acid Synthesis Inhibitors; D014498:Uracil; C012873:2'-deoxy-5'-adenosine monophosphate; D004247:DNA; D004259:DNA-Directed DNA Polymerase; D005092:Exonucleases