7U7D

Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mM Mn2+ for 30s

Summary for 7U7D

• Entry DOI: 10.2210/pdb7u7d/pdb
• Descriptor: DNA polymerase eta, DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'), ... (7 entities in total)
• Functional Keywords: polymerase, transferase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 55393.79

Authors

Chang, C.,Gao, Y. (deposition date: 2022-03-07, release date: 2022-05-04, Last modification date: 2023-10-18)

Primary citation

Chang, C.,Lee Luo, C.,Gao, Y.
In crystallo observation of three metal ion promoted DNA polymerase misincorporation.
Nat Commun, 13:2346-2346, 2022

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.

PubMed: 35487947
DOI: 10.1038/s41467-022-30005-3

Experimental method

X-RAY DIFFRACTION (1.57 Å)