7B0H

TgoT_6G12 Ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report



Literature

Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution.

Samson, C.Legrand, P.Tekpinar, M.Rozenski, J.Abramov, M.Holliger, P.Pinheiro, V.B.Herdwijn, P.Delarue, M.

(2020) Biomolecules 10

  • DOI: 10.3390/biom10121647
  • Primary Citation of Related Structures:  
    7B06, 7B08, 7B07, 7B0F, 7B0H, 7B0G

  • PubMed Abstract: 
  • Archaeal DNA polymerases from the B-family (polB) have found essential applications in biotechnology. In addition, some of their variants can accept a wide range of modified nucleotides or xenobiotic nucleotides, such as 1,5-anhydrohexitol nucleic ac ...

    Archaeal DNA polymerases from the B-family (polB) have found essential applications in biotechnology. In addition, some of their variants can accept a wide range of modified nucleotides or xenobiotic nucleotides, such as 1,5-anhydrohexitol nucleic acid (HNA), which has the unique ability to selectively cross-pair with DNA and RNA. This capacity is essential to allow the transmission of information between different chemistries of nucleic acid molecules. Variants of the archaeal polymerase from Thermococcus gorgonarius, TgoT, that can either generate HNA from DNA (TgoT_6G12) or DNA from HNA (TgoT_RT521) have been previously identified. To understand how DNA and HNA are recognized and selected by these two laboratory-evolved polymerases, we report six X-ray structures of these variants, as well as an in silico model of a ternary complex with HNA. Structural comparisons of the apo form of TgoT_6G12 together with its binary and ternary complexes with a DNA duplex highlight an ensemble of interactions and conformational changes required to promote DNA or HNA synthesis. MD simulations of the ternary complex suggest that the HNA-DNA hybrid duplex remains stable in the A-DNA helical form and help explain the presence of mutations in regions that would normally not be in contact with the DNA if it were not in the A-helical form. One complex with two incorporated HNA nucleotides is surprisingly found in a one nucleotide-backtracked form, which is new for a DNA polymerase. This information can be used for engineering a new generation of more efficient HNA polymerase variants.


    Organizational Affiliation

    Unit of Structural Dynamics of Biological Macromolecules, UMR 3528 du CNRS, Institut Pasteur, 25-28 rue du Dr Roux, 75015 Paris, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseEF773Thermococcus gorgonariusMutation(s): 18 
Gene Names: polpolA
EC: 2.7.7.7
Find proteins for P56689 (Thermococcus gorgonarius)
Explore P56689 
Go to UniProtKB:  P56689
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3')A, C13synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')D, G6synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.15 Å
      • R-Value Free: 0.247 
      • R-Value Work: 0.232 
      • R-Value Observed: 0.233 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 111.823α = 90
      b = 112.331β = 90
      c = 186.518γ = 90
      Software Package:
      Software NamePurpose
      BUSTERrefinement
      XSCALEdata scaling
      PDB_EXTRACTdata extraction
      XDSdata reduction
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Agence Nationale de la Recherche (ANR)BelgiumG0H7618N

      Revision History 

      • Version 1.0: 2021-01-13
        Type: Initial release