2KTQ

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

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

  • 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 ...

    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.


    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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (LARGE FRAGMENT OF DNA POLYMERASE I)A538Thermus aquaticusMutation(s): 0 
Gene Names: TAQpolApol1
EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus)
Explore P19821 
Go to UniProtKB:  P19821
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3')B12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')D13N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DCT
      Query on DCT

      Download Ideal Coordinates CCD File 
      A
      2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
      C9 H16 N3 O12 P3
      ARLKCWCREKRROD-POYBYMJQSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      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 = 108.414α = 90
      b = 108.414β = 90
      c = 89.843γ = 120
      Software Package:
      Software NamePurpose
      X-PLORrefinement

      Structure Validation

      View Full Validation Report



      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