title: The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β.
abstract: To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β (polβ), we report four crystal structures of polβ complexed with dG•dTTP and dA•dCTP mismatches in the presence of Mg2+ or Mn2+. The Mg(2+)-bound ground-state structures show that the dA•dCTP-Mg2+ complex adopts an 'intermediate' protein conformation while the dG•dTTP-Mg2+ complex adopts an open protein conformation. The Mn(2+)-bound 'pre-chemistry-state' structures show that the dA•dCTP-Mn2+ complex is structurally very similar to the dA•dCTP-Mg2+ complex, whereas the dG•dTTP-Mn2+ complex undergoes a large-scale conformational change to adopt a Watson-Crick-like dG•dTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that polβ increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, polβ appears to allow only a Watson-Crick-like conformation for purine•pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson-Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of polβ.
authors.affiliation: Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Myong-Chul
authors.initials: MC
authors.lastname: Koag
authors.affiliation: Department of Chemistry and Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden seongminlee@austin.utexas.edu.
authors.forename: Kwangho
authors.initials: K
authors.lastname: Nam
authors.affiliation: Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA seongminlee@austin.utexas.edu.
authors.forename: Seongmin
authors.initials: S
authors.lastname: Lee
mesh_terms: D020137:Base Pair Mismatch; D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry*; D019951:DNA Polymerase beta / Q000737:chemistry* / Q000378:metabolism; D004261:DNA Replication; D006801:Humans; D008274:Magnesium / Q000737:chemistry; D008345:Manganese / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation
chemical_list: D008345:Manganese; D004247:DNA; D019951:DNA Polymerase beta; D008274:Magnesium