5C53

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.300 
  • R-Value Observed: 0.301 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 U S A 112: 8596-8601

  • DOI: 10.1073/pnas.1421733112
  • Primary Citation of Related Structures:  
    5C52, 5C51, 5C53

  • 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 chain terminators of viral DNA synthesis ...

    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 and Toxicology, University of Texas Medical Branch, Galveston, TX 77555; Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555; ywyin@utmb.edu karen.anderson@yale.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-1 A1205Homo sapiensMutation(s): 0 
Gene Names: POLGMDP1POLG1POLGA
EC: 2.7.7.7
Find proteins for P54098 (Homo sapiens)
Explore P54098 
Go to UniProtKB:  P54098
NIH Common Fund Data Resources
PHAROS:  P54098
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pol gamma B BC903Homo sapiensMutation(s): 0 
Gene Names: POLG2MTPOLB
Find proteins for Q9UHN1 (Homo sapiens)
Explore Q9UHN1 
Go to UniProtKB:  Q9UHN1
NIH Common Fund Data Resources
PHAROS:  Q9UHN1
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (26-MER)T26DNA launch vector pDE-GFP2
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')P22DNA launch vector pDE-GFP2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4Y3
Query on 4Y3

Download Ideal Coordinates CCD File 
A
[[(2S,5R)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
C9 H15 F N3 O12 P3
ARRTZUVEPRJLPK-CAHLUQPWSA-N
 Ligand Interaction
DOC
Query on DOC

Download Ideal Coordinates CCD File 
P
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O6 P
RAJMXAZJKUGYGW-POYBYMJQSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.300 
  • R-Value Observed: 0.301 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.447α = 90
b = 217.447β = 90
c = 163.593γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release