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

EMBO J. 2015 Jul 14;34(14):1959-70. doi: 10.15252/embj.201591520. Epub 2015 Jun 8.


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.

Keywords: DNA replication; drug toxicity; human DNA polymerase gamma; mitochondrial toxicity; nucleoside reverse transcriptase inhibitors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA Polymerase gamma
  • DNA, Mitochondrial / metabolism
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / genetics
  • DNA-Directed DNA Polymerase / metabolism*
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Protein Conformation
  • Reverse Transcriptase Inhibitors / chemistry
  • Reverse Transcriptase Inhibitors / metabolism
  • Reverse Transcriptase Inhibitors / toxicity
  • Zalcitabine / chemistry
  • Zalcitabine / metabolism
  • Zalcitabine / toxicity*


  • DNA, Mitochondrial
  • Reverse Transcriptase Inhibitors
  • Zalcitabine
  • DNA Polymerase gamma
  • DNA-Directed DNA Polymerase
  • POLG protein, human

Associated data

  • PDB/4ZTU
  • PDB/4ZTZ