8PPU | pdb_00008ppu

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

• PDB DOI: https://doi.org/10.2210/pdb8PPU/pdb
• NAKB: 8PPU
• EM Map EMD-17816: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-07-10 Released: 2023-12-20 
• Deposition Author(s): Betancurt-Anzola, L., Martinez-Carranza, M., Zatopek, K.M., Gardner, A.F., Sauguet, L.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases.

Betancurt-Anzola, L., Martinez-Carranza, M., Delarue, M., Zatopek, K.M., Gardner, A.F., Sauguet, L.

(2023) Nat Commun 14: 8306-8306

• PubMed: 38097591 
• DOI: https://doi.org/10.1038/s41467-023-44125-x
• Primary Citation Related Structures: 
  8PPT, 8PPU, 8PPV


• 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.

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Organizational Affiliation: 
• Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
New England Biolabs France, 5 Rue Henri Auguste Desbruères, 91000, Évry-Courcouronnes, France.
Sorbonne Université, Collège Doctoral, ED 515, Paris, France.
New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA. [e-mail].
New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA. [e-mail].
Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 321.34 kDa 
• Atom Count: 19,649 
• Modeled Residue Count: 2,412 
• Deposited Residue Count: 2,761 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II small subunit	C [auth A]	662	Pyrococcus abyssi GE5	Mutation(s): 1  Gene Names: polB EC: 2.7.7.7 (UniProt), 3.1.11.1 (UniProt)
UniProt
Find proteins for Q9V2F3 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2F3  Go to UniProtKB:  Q9V2F3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase sliding clamp	D [auth C], E [auth D], F [auth E]	261	Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: pcn
UniProt
Find proteins for Q9UYX8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UYX8  Go to UniProtKB:  Q9UYX8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DP2	G [auth B]	1,270	Pyrococcus abyssi GE5	Mutation(s): 0  EC: 2.7.7.7 (UniProt), 3.1.11.1 (UniProt)
UniProt
Find proteins for Q9V2F4 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2F4  Go to UniProtKB:  Q9V2F4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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')	A [auth P]	21	Pyrococcus abyssi GE5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3')	B [auth T]	25	Pyrococcus abyssi GE5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	H [auth A], I [auth A], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Betancurt-Anzola, L., Martinez-Carranza, M., Zatopek, K.M., Gardner, A.F., Sauguet, L.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection