4ZTZ

Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.44 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase

Szymanski, M.R.Kuznestov, V.B.Shumate, C.K.Meng, Q.Lee, Y.-S.Patel, G.Patel, S.S.Yin, Y.W.

(2015) EMBO J 34: 1959

  • DOI: 10.15252/embj.201591520
  • Primary Citation of Related Structures:  
    4ZTZ, 4ZTU

  • PubMed Abstract: 
  • The human DNA polymerase gamma (Pol γ) is responsible for DNA replication in mitochondria. Pol γ is particularly susceptible to inhibition by dideoxynucleoside-based inhibitors designed to fight viral infection. Here, we report crystal structures of the replicating Pol γ-DNA complex bound to either substrate or zalcitabine, an inhibitor used for HIV reverse transcriptase ...

    The human DNA polymerase gamma (Pol γ) is responsible for DNA replication in mitochondria. Pol γ is particularly susceptible to inhibition by dideoxynucleoside-based inhibitors designed to fight viral infection. Here, we report crystal structures of the replicating Pol γ-DNA complex bound to either substrate or zalcitabine, an inhibitor used for HIV reverse transcriptase. The structures reveal that zalcitabine binds to the Pol γ active site almost identically to the substrate dCTP, providing a structural basis for Pol γ-mediated drug toxicity. When compared to the apo form, Pol γ undergoes intra- and inter-subunit conformational changes upon formation of the ternary complex with primer/template DNA and substrate. We also find that the accessory subunit Pol γB, which lacks intrinsic enzymatic activity and does not contact the primer/template DNA directly, serves as an allosteric regulator of holoenzyme activities. The structures presented here suggest a mechanism for processivity of the holoenzyme and provide a model for understanding the deleterious effects of Pol γ mutations in human disease. Crystal structures of the mitochondrial DNA polymerase, Pol γ, in complex with substrate or antiviral inhibitor zalcitabine provide a basis for understanding Pol γ-mediated drug toxicity.


    Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA ywyin@utmb.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-1 A1222Homo 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 BC472Homo 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 (25-MER)T27synthetic construct
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*AP*GP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3')P24synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

Download Ideal Coordinates CCD File 
A
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-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: 3.44 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.6α = 90
b = 217.6β = 90
c = 165.709γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy, Structure summary