title: Switching between polymerase and exonuclease sites in DNA polymerase ε.
abstract: The balance between exonuclease and polymerase activities promotes DNA synthesis over degradation when nucleotides are correctly added to the new strand by replicative B-family polymerases. Misincorporations shift the balance toward the exonuclease site, and the balance tips back in favor of DNA synthesis when the incorrect nucleotides have been removed. Most B-family DNA polymerases have an extended β-hairpin loop that appears to be important for switching from the exonuclease site to the polymerase site, a process that affects fidelity of the DNA polymerase. Here, we show that DNA polymerase ε can switch between the polymerase site and exonuclease site in a processive manner despite the absence of an extended β-hairpin loop. K967 and R988 are two conserved amino acids in the palm and thumb domain that interact with bases on the primer strand in the minor groove at positions n-2 and n-4/n-5, respectively. DNA polymerase ε depends on both K967 and R988 to stabilize the 3'-terminus of the DNA within the polymerase site and on R988 to processively switch between the exonuclease and polymerase sites. Based on a structural alignment with DNA polymerase δ, we propose that arginines corresponding to R988 might have a similar function in other B-family polymerases.
authors.affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden.
authors.forename: Rais A
authors.initials: RA
authors.lastname: Ganai
authors.affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden.
authors.forename: Göran O
authors.initials: GO
authors.lastname: Bylund
authors.affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden erik.johansson@medchem.umu.se.
authors.forename: Erik
authors.initials: E
authors.lastname: Johansson
mesh_terms: D019943:Amino Acid Substitution; D020134:Catalytic Domain; D004247:DNA / Q000096:biosynthesis / Q000378:metabolism; D004257:DNA Polymerase II / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D005090:Exodeoxyribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D004247:DNA; D004257:DNA Polymerase II; D005090:Exodeoxyribonucleases