Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 261504.91 
• Atom Count: 14619 
• Residue Count: 2217 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

4ZTU

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

• DOI: 10.2210/pdb4ZTU/pdb
• NDB: 4ZTU

• Classification: DNA Binding Protein/DNA
• Organism(s): Homo sapiens, Lobariella soredians
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): 2 


• Deposited: 2015-05-15 Released: 2015-09-23 
• Deposition Author(s): Szymanski, M.R., Kuznestov, V.B., Shumate, C.K., Meng, Q., Lee, Y.-S., Patel, G., Patel, S.S., Yin, Y.W.

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Experimental Data Snapshot

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

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

• PubMed: 26056153 
• DOI: 10.15252/embj.201591520
• Primary Citation of Related Structures:  
  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.

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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
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase subunit gamma-1	A	1222	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase subunit gamma-2, mitochondrial	B, C	472	Homo sapiens	Mutation(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
Molecule	Chains	Length	Organism
DNA (25-MER)	T	27	Lobariella soredians

Entity ID: 4
Molecule	Chains	Length	Organism
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')	P	24	Lobariella soredians

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DCT	A	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE C9 H16 N3 O12 P3 ARLKCWCREKRROD-POYBYMJQSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DOC	P	DNA LINKING	C9 H14 N3 O6 P		DC

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 = 217.575	α = 90.00
b = 217.575	β = 90.00
c = 168.277	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
HKL-2000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-15 
• Released Date: 2015-09-23 
• Deposition Author(s): Szymanski, M.R., Kuznestov, V.B., Shumate, C.K., Meng, Q., Lee, Y.-S., Patel, G., Patel, S.S., Yin, Y.W.

Revision History 

• Version 1.0: 2015-09-23
  Type: Initial release
• Version 1.1: 2019-03-13
  Type: Data collection, Derived calculations