8PPT

Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing a mismatch

Summary for 8PPT

• Entry DOI: 10.2210/pdb8ppt/pdb
• EMDB information: 17815
• Descriptor: DNA polymerase II small subunit, DNA polymerase sliding clamp, DNA (5'-D(P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*GP*CP*TP*TP*T)-3'), ... (7 entities in total)
• Functional Keywords: polymerase, dna, replication, pold, archaea, editing, proofreading, exonuclease, nuclease, dna binding protein
• Biological source: Pyrococcus abyssi GE5; More
• Total number of polymer chains: 7
• Total formula weight: 320374.65

Authors

Betancurt-Anzola, L.,Martinez-Carranza, M.,Zatopek, K.M.,Gardner, A.F.,Sauguet, L. (deposition date: 2023-07-10, release date: 2023-12-20, Last modification date: 2023-12-27)

Primary citation

Betancurt-Anzola, L.,Martinez-Carranza, M.,Delarue, M.,Zatopek, K.M.,Gardner, A.F.,Sauguet, L.
Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases.
Nat Commun, 14:8306-8306, 2023

PubMed Abstract: Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.

PubMed: 38097591
DOI: 10.1038/s41467-023-44125-x

Experimental method

ELECTRON MICROSCOPY (2.9 Å)