4ZTU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.299 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.316 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  

  • 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 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase subunit gamma-1
A
1222Homo sapiensMutation(s): 2 
Gene Names: POLG (MDP1, POLG1, POLGA)
EC: 2.7.7.7
Find proteins for P54098 (Homo sapiens)
Go to Gene View: POLG
Go to UniProtKB:  P54098
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase subunit gamma-2, mitochondrial
B, C
472Homo sapiensMutation(s): 0 
Gene Names: POLG2 (MTPOLB)
EC: 2.7.7.7
Find proteins for Q9UHN1 (Homo sapiens)
Go to Gene View: POLG2
Go to UniProtKB:  Q9UHN1
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)T27Lobariella soredians
Entity ID: 4
MoleculeChainsLengthOrganism
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')P24Lobariella soredians
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCT
Query on DCT

Download SDF File 
Download CCD File 
A
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.299 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 = 90.00
b = 217.575β = 90.00
c = 168.277γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release