1TAU

TAQ POLYMERASE (E.C.2.7.7.7)/DNA/B-OCTYLGLUCOSIDE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of Taq ploymerase with DNA at the polymerase active site.

Eom, S.H.Wang, J.Steitz, T.A.

(1996) Nature 382: 278-281

  • DOI: 10.1038/382278a0
  • Primary Citation of Related Structures:  
    1TAU

  • PubMed Abstract: 
  • The DNA polymerase from Thermus aquaticus (Taq polymerase) is homologous to Escherichia coli DNA polymerase I (Pol I) and likewise has domains responsible for DNA polymerase and 5' nuclease activities. The structures to the polymerase domains of Taq polymerase and of the Klenow fragment (KF) of Pol I are almost identical, whereas the structure of a vestigial editing 3'-5' exonuclease domain of Taq polymerase that lies between the other two domains is dramatically altered, resulting in the absence of this activity in the thermostable enzyme ...

    The DNA polymerase from Thermus aquaticus (Taq polymerase) is homologous to Escherichia coli DNA polymerase I (Pol I) and likewise has domains responsible for DNA polymerase and 5' nuclease activities. The structures to the polymerase domains of Taq polymerase and of the Klenow fragment (KF) of Pol I are almost identical, whereas the structure of a vestigial editing 3'-5' exonuclease domain of Taq polymerase that lies between the other two domains is dramatically altered, resulting in the absence of this activity in the thermostable enzyme. The structures have been solved for editing complexes between KF and single-stranded DNA and for duplex DNA with a 3' overhanging single strand, but not for a complex containing duplex DNA at the polymerase active-site. Here we present the co-crystal structure of Taq polymerase with a blunt-ended duplex DNA bound to the polymerase active-site cleft; the DNA neither bends nor goes through the large polymerase cleft, and the structural form of the bound DNA is between the B and A forms. A wide minor groove allows access to protein side chains that hydrogen-bond to the N3 of purines and the O2 of pyrimidines at the blunt-end terminus. Part of the DNA bound to the polymerase site shares a common binding site with DNA bound to the exonuclease site, but they are translated relative to each other by several angstroms along their helix axes.


    Related Citations: 
    • Crystal Structure of Thermus Aquatics DNA Polymerase
      Kim, Y., Eom, S.H., Wang, J., Lee, D.-S., Suh, S.W., Steitz, T.A.
      (1995) Nature 376: 612
    • Isolation, Characterization, and Expression in Escherichia Coli of the DNA Polymerase Gene From Thermus Aquaticus
      Lawyer, F.C., Stoffel, S., Saiki, R.K., Myambo, K., Drummond, R., Gelfand, D.H.
      (1989) J Biol Chem 264: 6427

    Organizational Affiliation

    Department of Molecular Biophysics, Yale University, New Haven, Connecticut 06520-811, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (TAQ POLYMERASE)C [auth A]832Thermus aquaticusMutation(s): 0 
Gene Names: polApol1
EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus)
Explore P19821 
Go to UniProtKB:  P19821
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*GP*AP*TP*CP*CP*G)-3')A [auth T]8N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*GP*AP*TP*CP*GP*C)-3')B [auth P]8N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      BGL
      Query on BGL

      Download Ideal Coordinates CCD File 
      D [auth A]2-O-octyl-beta-D-glucopyranose
      C14 H28 O6
      BVHPDIWLWHHJPD-RKQHYHRCSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      E [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.00 Å
      • R-Value Free: 0.305 
      • R-Value Work: 0.244 
      • Space Group: P 31 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 107.6α = 90
      b = 107.6β = 90
      c = 170.01γ = 120
      Software Package:
      Software NamePurpose
      X-PLORrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1997-04-18
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2017-03-01
        Changes: Database references
      • Version 1.4: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Data collection, Derived calculations, Structure summary