4QW9

TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)FTC-PPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.

Gaur, V.Vyas, R.Fowler, J.D.Efthimiopoulos, G.Feng, J.Y.Suo, Z.

(2014) Nucleic Acids Res 42: 9984-9995

  • DOI: 10.1093/nar/gku709
  • Primary Citation of Related Structures:  
    4QW8, 4QW9, 4QWA, 4QWB, 4QWC, 4QWD, 4QWE

  • PubMed Abstract: 
  • Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis ...

    Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) and L-thymidine (telbivudine) have been widely used as antiviral drugs for years. Here we report seven high-resolution ternary crystal structures of a prototype Y-family DNA polymerase, DNA, and D-dCTP, D-dCDP, L-dCDP, or the diphosphates and triphosphates of lamivudine and emtricitabine. These structures reveal that relative to D-dCTP, each of these L-nucleotides has its sugar ring rotated by 180° with an unusual O4'-endo sugar puckering and exhibits multiple triphosphate-binding conformations within the active site of the polymerase. Such rare binding modes significantly decrease the incorporation rates and efficiencies of these L-nucleotides catalyzed by the polymerase.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA suo.3@osu.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVA349Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: dbhdpo4SSO2448
EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')B [auth C]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')C [auth D]16N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      0G4 (Subject of Investigation/LOI)
      Query on 0G4

      Download Ideal Coordinates CCD File 
      D [auth A][[[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy -oxidanyl-phosphoryl]amino]phosphonic acid
      C8 H14 F N4 O11 P3 S
      LBSQECIRXSOKHJ-NTSWFWBYSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      E [auth A], F [auth A], G [auth A]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.40 Å
      • R-Value Free: 0.270 
      • R-Value Work: 0.242 
      • R-Value Observed: 0.245 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 96.8α = 90
      b = 101.9β = 90
      c = 52.54γ = 90
      Software Package:
      Software NamePurpose
      MOLREPphasing
      REFMACrefinement
      MOSFLMdata reduction
      SCALAdata scaling

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      • Deposited Date: 2014-07-16 
      • Released Date: 2014-08-27 
      • Deposition Author(s): Gaur, V., Suo, Z.

      Revision History  (Full details and data files)

      • Version 1.0: 2014-08-27
        Type: Initial release
      • Version 1.1: 2014-09-17
        Changes: Database references