4ZTU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.316 

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

  • 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-11,222Homo sapiensMutation(s): 2 
Gene Names: POLGMDP1POLG1POLGA
EC: 2.7.7.7
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
DNA polymerase subunit gamma-2, mitochondrial
B, C
472Homo sapiensMutation(s): 0 
Gene Names: POLG2MTPOLB
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (25-MER)D [auth T]27synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
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')E [auth P]24synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.316 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.575α = 90
b = 217.575β = 90
c = 168.277γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Derived calculations
  • Version 1.2: 2020-02-19
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations