{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Chang C"],"funding":["Welch Foundation","NIGMS NIH HHS","Cancer Prevention and Research Institute of Texas"],"pagination":["2346"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9054841"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["13(1)"],"pubmed_abstract":["Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis."],"journal":["Nature communications"],"pubmed_title":["In crystallo observation of three metal ion promoted DNA polymerase misincorporation."],"pmcid":["PMC9054841"],"funding_grant_id":["RR190046","C-2033-20200401","T32 GM008280"],"pubmed_authors":["Lee Luo C","Gao Y","Chang C"],"additional_accession":[]},"is_claimable":false,"name":"In crystallo observation of three metal ion promoted DNA polymerase misincorporation.","description":"Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Apr","modification":"2026-05-31T06:06:11.119Z","creation":"2025-02-19T01:55:24.463Z"},"accession":"S-EPMC9054841","cross_references":{"pubmed":["35487947"],"doi":["10.1038/s41467-022-30005-3"]}}