8PPU image
Entry Detail
PDB ID:
8PPU
EMDB ID:
Title:
Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing three consecutive mismatches
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-07-10
Release Date:
2023-12-20
Method Details:
Experimental Method:
Resolution:
3.02 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA polymerase II small subunit
Mutations:H451A
Chain IDs:C (auth: A)
Chain Length:662
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Description:DP2
Chain IDs:G (auth: B)
Chain Length:1270
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Description:DNA polymerase sliding clamp
Chain IDs:D (auth: C), E (auth: D), F (auth: E)
Chain Length:261
Number of Molecules:3
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(C7R)P*(PST)P*(PST)P*(PST))-3')
Chain IDs:A (auth: P)
Chain Length:21
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3')
Chain IDs:B (auth: T)
Chain Length:25
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Primary Citation
Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases.
Nat Commun 14 8306 8306 (2023)
PMID: 38097591 DOI: 10.1038/s41467-023-44125-x

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures