title: Exonuclease processivity of archaeal replicative DNA polymerase in association with PCNA is expedited by mismatches in DNA.
abstract: Family B DNA polymerases comprise polymerase and 3' ->5' exonuclease domains, and detect a mismatch in a newly synthesized strand to remove it in cooperation with Proliferating cell nuclear antigen (PCNA), which encircles the DNA to provide a molecular platform for efficient protein-protein and protein-DNA interactions during DNA replication and repair. Once the repair is completed, the enzyme must stop the exonucleolytic process and switch to the polymerase mode. However, the cue to stop the degradation is unclear. We constructed several PCNA mutants and found that the exonuclease reaction was enhanced in the mutants lacking the conserved basic patch, located on the inside surface of PCNA. These mutants may mimic the Pol/PCNA complex processing the mismatched DNA, in which PCNA cannot interact rigidly with the irregularly distributed phosphate groups outside the dsDNA. Indeed, the exonuclease reaction with the wild type PCNA was facilitated by mismatched DNA substrates. PCNA may suppress the exonuclease reaction after the removal of the mismatched nucleotide. PCNA seems to act as a "brake" that stops the exonuclease mode of the DNA polymerase after the removal of a mismatched nucleotide from the substrate DNA, for the prompt switch to the DNA polymerase mode.
authors.affiliation: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Yoda
authors.affiliation: Hitachi, Ltd. Research &Development Group, 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan.
authors.forename: Maiko
authors.initials: M
authors.lastname: Tanabe
authors.affiliation: Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan.
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Tsuji
authors.affiliation: Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan.
authors.forename: Takao
authors.initials: T
authors.lastname: Yoda
authors.affiliation: Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan.
authors.forename: Sonoko
authors.initials: S
authors.lastname: Ishino
authors.affiliation: Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Shirai
authors.affiliation: Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan.
authors.forename: Yoshizumi
authors.initials: Y
authors.lastname: Ishino
authors.affiliation: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
authors.forename: Haruko
authors.initials: H
authors.lastname: Takeyama
authors.affiliation: Hitachi, Ltd. Research &Development Group, 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Nishida
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D001105:Archaea / Q000201:enzymology; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics; D004247:DNA / Q000737:chemistry; D053843:DNA Mismatch Repair / Q000235:genetics; D019951:DNA Polymerase beta / Q000737:chemistry* / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000235:genetics; D018809:Proliferating Cell Nuclear Antigen / Q000737:chemistry* / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; D018809:Proliferating Cell Nuclear Antigen; D004247:DNA; D019951:DNA Polymerase beta