Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.87 kDa 
• Atom Count: 4631 
• Modelled Residue Count: 553 
• Deposited Residue Count: 563 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2KTQ

OPEN TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS

• PDB DOI: 10.2210/pdb2KTQ/pdb
• NDB: PD0030

• Classification: TRANSFERASE/DNA
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-07-30 Released: 1999-01-13 
• Deposition Author(s): Li, Y., Waksman, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Literature

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

Li, Y., Korolev, S., Waksman, G.

(1998) EMBO J 17: 7514-7525

• PubMed: 9857206 
• DOI: 10.1093/emboj/17.24.7514
• Primary Citation of Related Structures:  
  2KTQ, 3KTQ, 4KTQ


• PubMed Abstract: 
  

The crystal structures of two ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA and dideoxycytidine triphosphate, and that of a binary complex of the same enzyme with a primer/template DNA, were determined to a resolution of 2.3, 2.3 and 2.5 A, respectively. One ternary complex structure differs markedly from the two other structures by a large reorientation of the tip of the fingers domain. This structure, designated 'closed', represents the ternary polymerase complex caught in the act of incorporating a nucleotide. In the two other structures, the tip of the fingers domain is rotated outward by 46 degrees ('open') in an orientation similar to that of the apo form of Klentaq1. These structures provide the first direct evidence in DNA polymerase I enzymes of a large conformational change responsible for assembling an active ternary complex.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Campus Box 8231, 660 South Euclid Avenue, St Louis, MO 63110, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (LARGE FRAGMENT OF DNA POLYMERASE I)	C [auth A]	538	Thermus aquaticus	Mutation(s): 0  Gene Names: TAQ, polA, pol1 EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus) Explore P19821  Go to UniProtKB:  P19821

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3')	A [auth B]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')	B [auth D]	13	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCT	E [auth A]	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE C9 H16 N3 O12 P3 ARLKCWCREKRROD-POYBYMJQSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.414	α = 90
b = 108.414	β = 90
c = 89.843	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-30 
• Released Date: 1999-01-13 
Deposition Author(s): Li, Y., Waksman, G.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description