4QWB

CRYSTAL STRUCTURE of DPO4 LINKER REGION P236A MUTANT WITH AN INCOMING D-dCDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


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 IVA343Saccharolobus solfataricus P2Mutation(s): 1 
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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*(DOC))-3')B13N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')C18N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      YYY (Subject of Investigation/LOI)
      Query on YYY

      Download Ideal Coordinates CCD File 
      D [auth A]DEOXYCYTIDINE DIPHOSPHATE
      C9 H15 N3 O10 P2
      FTDHDKPUHBLBTL-SHYZEUOFSA-N
       Ligand Interaction
      GOL
      Query on GOL

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

      Download Ideal Coordinates CCD File 
      H [auth A], I [auth A], J [auth A], K [auth A]ACETATE ION
      C2 H3 O2
      QTBSBXVTEAMEQO-UHFFFAOYSA-M
       Ligand Interaction
      CA
      Query on CA

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.80 Å
      • R-Value Free: 0.271 
      • R-Value Work: 0.224 
      • R-Value Observed: 0.226 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 96.95α = 90
      b = 102.34β = 90
      c = 52.73γ = 90
      Software Package:
      Software NamePurpose
      PHASERphasing
      REFMACrefinement
      MOSFLMdata reduction
      SCALAdata scaling

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      • Deposited Date: 2014-07-16 
      • Released Date: 2014-08-27 
      • Deposition Author(s): Vyas, R., 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