4QWA

TERNARY CRYSTAL STRUCTURES OF A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS in COMPLEX WITH DNA AND (-)3TC-DP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


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
  • Structures With Same Primary Citation

  • 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 incorpor ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
A
349Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: dbhdpo4SSO2448
EC: 2.7.7.7
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W02
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')D16N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3')C13N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G8
Query on 0G8

Download CCD File 
A
[(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl trihydrogen diphosphate
C8 H13 N3 O9 P2 S
AAHOBGDTTMOZKD-NKWVEPMBSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
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: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.179α = 90
b = 102.644β = 90
c = 52.586γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

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