7U7D

In crystallo observation of three metal ion promoted DNA polymerase misincorporation.

(2022) Nat Commun 13: 2346-2346

• PubMed: 35487947 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1038/s41467-022-30005-3
• Primary Citation of Related Structures:  
  7U72, 7U73, 7U74, 7U75, 7U76, 7U77, 7U78, 7U79, 7U7A, 7U7B, 7U7C, 7U7D, 7U7E, 7U7F, 7U7G, 7U7I, 7U7J, 7U7K, 7U7L, 7U7R, 7U7S, 7U7T, 7U7U, 7U7V, 7U7W, 7U7X, 7U7Y, 7U7Z, 7U80, 7U81, 7U82, 7U83, 7U84


• 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.

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Organizational Affiliation: 

Department of Biosciences, Rice University, Houston, TX, 77005, USA.