4QWE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

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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

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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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97W02
Protein Feature View
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  • Reference Sequence

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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

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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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FTD
Query on FTD

Download Ideal Coordinates CCD File 
D [auth A][(2R,5S)-5-(4-amino-5-fluoro-2-oxo-3,6-dihydropyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl trihydrogen diphosphate
C8 H14 F N3 O9 P2 S
DSUZHKWUVJBGFZ-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: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.698α = 90
b = 102.432β = 90
c = 52.46γ = 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

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