Crystal Structure of human DNA polymerase gamma accessory subunit

Experimental Data Snapshot

  • Resolution: 3.15 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.217 

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A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase

Fan, L.Kim, S.Farr, C.L.Schaefer, K.T.Randolph, K.M.Tainer, J.A.Kaguni, L.S.

(2006) J Mol Biol 358: 1229-1243

  • DOI: https://doi.org/10.1016/j.jmb.2006.02.073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Mitochondrial DNA polymerase (pol gamma) is the sole DNA polymerase responsible for replication and repair of animal mitochondrial DNA. Here, we address the molecular mechanism by which the human holoenzyme achieves high processivity in nucleotide polymerization. We have determined the crystal structure of human pol gamma-beta, the accessory subunit that binds with high affinity to the catalytic core, pol gamma-alpha, to stimulate its activity and enhance holoenzyme processivity. We find that human pol gamma-beta shares a high level of structural similarity to class IIa aminoacyl tRNA synthetases, and forms a dimer in the crystal. A human pol gamma/DNA complex model was developed using the structures of the pol gamma-beta dimer and the bacteriophage T7 DNA polymerase ternary complex, which suggests multiple regions of subunit interaction between pol gamma-beta and the human catalytic core that allow it to encircle the newly synthesized double-stranded DNA, and thereby enhance DNA binding affinity and holoenzyme processivity. Biochemical properties of a novel set of human pol gamma-beta mutants are explained by and test the model, and elucidate the role of the accessory subunit as a novel type of processivity factor in stimulating pol gamma activity and in enhancing processivity.

  • Organizational Affiliation

    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92034, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase gamma subunit 2
A, B, C, D
474Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHN1 (Homo sapiens)
Explore Q9UHN1 
Go to UniProtKB:  Q9UHN1
GTEx:  ENSG00000256525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHN1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.15 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.217 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.79α = 90
b = 101.79β = 90
c = 170.277γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description