3O59

DNA polymerase D large subunit DP2(1-300) from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb3O59/pdb

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


• Deposited: 2010-07-28 Released: 2011-01-05 
• Deposition Author(s): Yokoyama, H., Shen, Y., Matsui, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.272 
• R-Value Work: 0.206 
• R-Value Observed: 0.212 

Literature

Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii

Matsui, I., Urushibata, Y., Shen, Y., Matsui, E., Yokoyama, H.

(2011) FEBS Lett 585: 452-458

• PubMed: 21192935 
• DOI: https://doi.org/10.1016/j.febslet.2010.12.040
• Primary Citation of Related Structures:  
  3O59


• PubMed Abstract: 
  

  Archaea-specific D-family DNA polymerase forms a heterotetramer consisting of two large polymerase subunits and two small exonuclease subunits. The N-terminal (1-300) domain structure of the large subunit was determined by X-ray crystallography, although ∼50 N-terminal residues were disordered. The determined structure consists of nine alpha helices and three beta strands. We also identified the DNA-binding ability of the domain by SPR measurement. The N-terminal (1-100) region plays crucial roles in the folding of the large subunit dimer by connecting the ∼50 N-terminal residues with their own catalytic region (792-1163).

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Organizational Affiliation: 

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.91 kDa 
• Atom Count: 2,016 
• Modelled Residue Count: 244 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II large subunit	A [auth X]	300	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH0121 EC: 2.7.7.7
UniProt
Find proteins for O57861 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57861  Go to UniProtKB:  O57861

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.272 
• R-Value Work: 0.206 
• R-Value Observed: 0.212 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.042	α = 90
b = 54.042	β = 90
c = 173.335	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-05 
Deposition Author(s): Yokoyama, H., Shen, Y., Matsui, I.

Revision History  

• Version 1.0: 2011-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance