3IKM

Crystal structure of human mitochondrial DNA polymerase holoenzyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.284 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural insight into processive human mitochondrial DNA synthesis and disease-related polymerase mutations.

Lee, Y.S., Kennedy, W.D., Yin, Y.W.

(2009) Cell 139: 312-324

  • DOI: 10.1016/j.cell.2009.07.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Human mitochondrial DNA polymerase (Pol gamma) is the sole replicase in mitochondria. Pol gamma is vulnerable to nonselective antiretroviral drugs and is increasingly associated with mutations found in patients with mitochondriopathies. We determined ...

    Human mitochondrial DNA polymerase (Pol gamma) is the sole replicase in mitochondria. Pol gamma is vulnerable to nonselective antiretroviral drugs and is increasingly associated with mutations found in patients with mitochondriopathies. We determined crystal structures of the human heterotrimeric Pol gamma holoenzyme and, separately, a variant of its processivity factor, Pol gammaB. The holoenzyme structure reveals an unexpected assembly of the mitochondrial DNA replicase where the catalytic subunit Pol gammaA interacts with its processivity factor primarily via a domain that is absent in all other DNA polymerases. This domain provides a structural module for supporting both the intrinsic processivity of the catalytic subunit alone and the enhanced processivity of holoenzyme. The Pol gamma structure also provides a context for interpreting the phenotypes of disease-related mutations in the polymerase and establishes a foundation for understanding the molecular basis of toxicity of anti-retroviral drugs targeting HIV reverse transcriptase.

    Organizational Affiliation: 

    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase subunit gamma-1
A, D
1172Homo sapiensMutation(s): 0 
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
B, C, E, F
427Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.284 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 138.394α = 90.00
b = 138.394β = 90.00
c = 226.312γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary