5C51

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.316 

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 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
DNA polymerase subunit gamma-2, mitochondrial BC485Homo sapiensMutation(s): 0 
Gene Names: POLG2MTPOLB
EC: 2.7.7.7
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 (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
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
DNAT25DNA launch vector pDE-GFP2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1RY
Query on 1RY

Download Ideal Coordinates 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
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: 3.43 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.316 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.049α = 90
b = 215.049β = 90
c = 161.692γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data 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: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Other