5IHE | pdb_00005ihe

D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)

• PDB DOI: https://doi.org/10.2210/pdb5IHE/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-29 Released: 2016-08-31 
• Deposition Author(s): Sauguet, L., Raia, P., De Larue, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.225 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.

Sauguet, L., Raia, P., Henneke, G., Delarue, M.

(2016) Nat Commun 7: 12227-12227

• PubMed: 27548043 
• DOI: https://doi.org/10.1038/ncomms12227
• Primary Citation Related Structures: 
  5IHE, 5IJL


• PubMed Abstract: 
  

  Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 Å resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same 'double-psi β-barrel' architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs.

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Organizational Affiliation: 
• Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, 75015 Paris, France.
Pierre and Marie Curie University, Paris 6, 75006 Paris, France.
Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.
UBO, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.
CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.43 kDa 
• Atom Count: 7,181 
• Modeled Residue Count: 882 
• Deposited Residue Count: 950 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II small subunit	A, B	475	Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: polB, PYRAB01210, PAB2266 EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (UniProt)
UniProt
Find proteins for Q9V2F3 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2F3  Go to UniProtKB:  Q9V2F3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D5M	C [auth A], I [auth B]	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE C10 H14 N5 O6 P KHWCHTKSEGGWEX-RRKCRQDMSA-N
ZN	E [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	G [auth A], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	D [auth A], J [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	F [auth A], H [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.225 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.969	α = 90
b = 91.415	β = 90
c = 145.209	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Sauguet, L., Raia, P., De Larue, M.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2016-09-07
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations