5C51

Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.426 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.315 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.

Sohl, C.D.Szymanski, M.R.Mislak, A.C.Shumate, C.K.Amiralaei, S.Schinazi, R.F.Anderson, K.S.Yin, Y.W.

(2015) Proc.Natl.Acad.Sci.USA 112: 8596-8601

  • DOI: 10.1073/pnas.1421733112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleoside analog reverse transcriptase inhibitors (NRTIs) are the essential components of highly active antiretroviral (HAART) therapy targeting HIV reverse transcriptase (RT). NRTI triphosphates (NRTI-TP), the biologically active forms, act as chai ...

    Nucleoside analog reverse transcriptase inhibitors (NRTIs) are the essential components of highly active antiretroviral (HAART) therapy targeting HIV reverse transcriptase (RT). NRTI triphosphates (NRTI-TP), the biologically active forms, act as chain terminators of viral DNA synthesis. Unfortunately, NRTIs also inhibit human mitochondrial DNA polymerase (Pol γ), causing unwanted mitochondrial toxicity. Understanding the structural and mechanistic differences between Pol γ and RT in response to NRTIs will provide invaluable insight to aid in designing more effective drugs with lower toxicity. The NRTIs emtricitabine [(-)-2,3'-dideoxy-5-fluoro-3'-thiacytidine, (-)-FTC] and lamivudine, [(-)-2,3'-dideoxy-3'-thiacytidine, (-)-3TC] are both potent RT inhibitors, but Pol γ discriminates against (-)-FTC-TP by two orders of magnitude better than (-)-3TC-TP. Furthermore, although (-)-FTC-TP is only slightly more potent against HIV RT than its enantiomer (+)-FTC-TP, it is discriminated by human Pol γ four orders of magnitude more efficiently than (+)-FTC-TP. As a result, (-)-FTC is a much less toxic NRTI. Here, we present the structural and kinetic basis for this striking difference by identifying the discriminator residues of drug selectivity in both viral and human enzymes responsible for substrate selection and inhibitor specificity. For the first time, to our knowledge, this work illuminates the mechanism of (-)-FTC-TP differential selectivity and provides a structural scaffold for development of novel NRTIs with lower toxicity.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase subunit gamma-1
A
1205Homo sapiensMutation(s): 0 
Gene Names: POLG (MDP1, POLG1, POLGA)
EC: 2.7.7.7
Find proteins for P54098 (Homo sapiens)
Go to Gene View: POLG
Go to UniProtKB:  P54098
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase subunit gamma-2, mitochondrial
B, C
485Homo sapiensMutation(s): 0 
Gene Names: POLG2 (MTPOLB)
EC: 2.7.7.7
Find proteins for Q9UHN1 (Homo sapiens)
Go to Gene View: POLG2
Go to UniProtKB:  Q9UHN1
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*(AD)P*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')P22Virus Chimp162
Entity ID: 4
MoleculeChainsLengthOrganism
DNAT25DNA launch vector pDE-GFP2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1RY
Query on 1RY

Download SDF File 
Download CCD File 
A
[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
C8 H13 F N3 O12 P3 S
WIEOLFZNMKSGEX-NTSWFWBYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.426 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.315 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 215.049α = 90.00
b = 215.049β = 90.00
c = 161.692γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Other