4N5S

Ternary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA and ddCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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Literature

A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase.

Wu, E.Y.Walsh, A.R.Materne, E.C.Hiltner, E.P.Zielinski, B.Miller, B.R.Mawby, L.Modeste, E.Parish, C.A.Barnes, W.M.Kermekchiev, M.B.

(2015) Biochemistry 54: 881-889

  • DOI: 10.1021/bi501198f
  • Primary Citation of Related Structures:  
    4XIU, 4N56, 4N5S

  • PubMed Abstract: 
  • Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA ...

    Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA. To understand why a conservative change to the enzyme over 20 Å from the active site can have a large impact on its activity at low temperature, we solved the X-ray crystal structure of the large (5'-to-3' exonuclease-deleted) fragment of Taq DNA polymerase containing the cold-sensitive mutation in the ternary (E-DNA-ddNTP) and binary (E-DNA) complexes. The I707L KlenTaq1 ternary complex was identical to the wild-type in the closed conformation except for the mutation and a rotamer change in nearby phenylalanine 749, suggesting that the enzyme should remain active. However, soaking out of the nucleotide substrate at low temperature results in an altered binary complex made possible by the rotamer change at F749 near the tip of the polymerase O-helix. Surprisingly, two adenosines in the 5'-template overhang fill the vacated active site by stacking with the primer strand, thereby blocking the active site at low temperature. Replacement of the two overhanging adenosines with pyrimidines substantially increased activity at room temperature by keeping the template overhang out of the active site, confirming the importance of base stacking. These results explain the cold-sensitive phenotype of the I707L mutation in KlenTaq1 and serve as an example of a large conformational change affected by a conservative mutation.


    Organizational Affiliation

    Department of Biology and ‡Department of Chemistry, University of Richmond , Richmond, Virginia 23173, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase I, thermostableC [auth A]553Thermus aquaticusMutation(s): 1 
Gene Names: polApol1
EC: 2.7.7.7
UniProt
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
    5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'A [auth B]12N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'B [auth C]16N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 6 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DCT (Subject of Investigation/LOI)
      Query on DCT

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

      Download Ideal Coordinates CCD File 
      L [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
      C8 H18 N2 O4 S
      JKMHFZQWWAIEOD-UHFFFAOYSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      O [auth A]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ACT
      Query on ACT

      Download Ideal Coordinates CCD File 
      M [auth A], N [auth A]ACETATE ION
      C2 H3 O2
      QTBSBXVTEAMEQO-UHFFFAOYSA-M
       Ligand Interaction
      MN
      Query on MN

      Download Ideal Coordinates CCD File 
      D [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      E [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.67 Å
      • R-Value Free: 0.192 
      • R-Value Work: 0.161 
      • R-Value Observed: 0.163 
      • Space Group: P 31 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 107.657α = 90
      b = 107.657β = 90
      c = 89.659γ = 120
      Software Package:
      Software NamePurpose
      SERGUIdata collection
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      • Deposited Date: 2013-10-10 
      • Released Date: 2015-01-21 
      • Deposition Author(s): Wu, E.Y.

      Revision History  (Full details and data files)

      • Version 1.0: 2015-01-21
        Type: Initial release
      • Version 1.1: 2015-02-11
        Changes: Database references