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 

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This is version 2.0 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: https://doi.org/10.1073/pnas.1421733112
  • Primary Citation of Related Structures:  
    5C51, 5C52, 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. 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-11,205Homo sapiensMutation(s): 0 
Gene Names: POLGMDP1POLG1POLGA
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt), 4.2.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P54098 (Homo sapiens)
Explore P54098 
Go to UniProtKB:  P54098
PHAROS:  P54098
GTEx:  ENSG00000140521 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54098
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pol gamma B
B, C
903Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHN1 (Homo sapiens)
Explore Q9UHN1 
Go to UniProtKB:  Q9UHN1
PHAROS:  Q9UHN1
GTEx:  ENSG00000256525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHN1
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (26-MER)D [auth T]26DNA launch vector pDE-GFP2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
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')E [auth P]22DNA launch vector pDE-GFP2
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  • Reference Sequence
Small Molecules
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 2.0: 2024-03-06
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary