Summary information and primary citation
- PDB-id
- 7u83; SNAP-derived features in text and JSON formats;
DNAproDB
- Class
- transferase-DNA
- Method
- X-ray (1.55 Å)
- Summary
- Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 3.0 mm mn2+ for 600s
- Reference
- Chang C, Lee Luo C, Gao Y (2022): "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3.
- 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.
