8G5K

Cryo-EM structure of the Wedge Alignment Complex (VIII) of Human Mitochondrial DNA Polymerase Gamma

Summary for 8G5K

• Entry DOI: 10.2210/pdb8g5k/pdb
• EMDB information: 29747
• Descriptor: DNA polymerase subunit gamma-1, DNA polymerase subunit gamma-2, mitochondrial, Mismatched Primer DNA, ... (4 entities in total)
• Functional Keywords: mitochondrial dna polymerase, dna proofreading, wedge alignment, replication, replication-dna complex, replication/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 263815.80

Authors

Nayak, A.R.,Buchel, G.,Herbine, K.H.,Sarfallah, A.,Sokolova, V.O.,Zamudio-Ochoa, A.,Temiakov, D. (deposition date: 2023-02-13, release date: 2024-01-10)

Primary citation

Buchel, G.,Nayak, A.R.,Herbine, K.,Sarfallah, A.,Sokolova, V.O.,Zamudio-Ochoa, A.,Temiakov, D.
Structural basis for DNA proofreading.
Nat Commun, 14:8501-8501, 2023

PubMed Abstract: DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement of the mismatched base into the exonuclease site. Altogether, our findings suggest a conserved 'bolt-action' mechanism of proofreading based on iterative cycles of DNAP translocation without dissociation from the DNA, facilitating primer transfer between catalytic sites. Functional assays and mutagenesis corroborate this mechanism, connecting pathogenic mutations to crucial structural elements in proofreading steps.

PubMed: 38151585
DOI: 10.1038/s41467-023-44198-8

Experimental method

ELECTRON MICROSCOPY (2.9 Å)