Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.30 kDa 
• Atom Count: 6157 
• Modelled Residue Count: 729 
• Deposited Residue Count: 774 
• Unique protein chains: 1

1WN7

Crystal structure of archaeal family B DNA polymerase mutant

• PDB DOI: 10.2210/pdb1WN7/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-28 Released: 2005-08-02 
• Deposition Author(s): Kuroita, T., Matsumura, H., Yokota, N., Hashimoto, H., Imanaka, T., Inoue, T., Kai, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.306 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Structural Mechanism for Coordination of Proofreading and Polymerase Activities in Archaeal DNA Polymerases

Kuroita, T., Matsumura, H., Yokota, N., Kitabayashi, M., Hashimoto, H., Inoue, T., Imanaka, T., Kai, Y.

(2005) J Mol Biol 351: 291-298

• PubMed: 16019029 
• DOI: 10.1016/j.jmb.2005.06.015
• Primary Citation of Related Structures:  
  1WN7


• PubMed Abstract: 
  

A novel mechanism for controlling the proofreading and polymerase activities of archaeal DNA polymerases was studied. The 3'-5'exonuclease (proofreading) activity and PCR performance of the family B DNA polymerase from Thermococcus kodakaraensis KOD1 (previously Pyrococcus kodakaraensis KOD1) were altered efficiently by mutation of a "unique loop" in the exonuclease domain. Interestingly, eight different H147 mutants showed considerable variations in respect to their 3'-5'exonuclease activity, from 9% to 276%, as against that of the wild-type (WT) enzyme. We determined the 2.75A crystal structure of the H147E mutant of KOD DNA polymerase that shows 30% of the 3'-5'exonuclease activity, excellent PCR performance and WT-like fidelity. The structural data indicate that the properties of the H147E mutant were altered by a conformational change of the Editing-cleft caused by an interaction between the unique loop and the Thumb domain. Our data suggest that electrostatic and hydrophobic interactions between the unique loop of the exonuclease domain and the tip of the Thumb domain are essential for determining the properties of these DNA polymerases.

---

Related Citations: 

• Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1
  Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Inoue, T., Kai, Y.
  (2001) J Mol Biol 306: 469

---

Organizational Affiliation: 

Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24 Toyo-cho, Tsuruga, Fukui 914-0047, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Family B DNA Polymerase	A	774	Thermococcus kodakarensis KOD1	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore D0VWU9  Go to UniProtKB:  D0VWU9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.306 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.344	α = 90
b = 111.131	β = 90
c = 111.559	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-28 
• Released Date: 2005-08-02 
Deposition Author(s): Kuroita, T., Matsumura, H., Yokota, N., Hashimoto, H., Imanaka, T., Inoue, T., Kai, Y.

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance