Apo structure of a UbiA homolog from Aeropyrum pernix K1

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report

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Structural insights into ubiquinone biosynthesis in membranes.

Cheng, W.Li, W.

(2014) Science 343: 878-881

  • DOI: https://doi.org/10.1126/science.1246774
  • Primary Citation of Related Structures:  
    4OD4, 4OD5

  • PubMed Abstract: 

    Biosynthesis of ubiquinones requires the intramembrane UbiA enzyme, an archetypal member of a superfamily of prenyltransferases that generates lipophilic aromatic compounds. Mutations in eukaryotic superfamily members have been linked to cardiovascular degeneration and Parkinson's disease. To understand how quinones are produced within membranes, we report the crystal structures of an archaeal UbiA in its apo and substrate-bound states at 3.3 and 3.6 angstrom resolution, respectively. The structures reveal nine transmembrane helices and an extramembrane cap domain that surround a large central cavity containing the active site. To facilitate the catalysis inside membranes, UbiA has an unusual active site that opens laterally to the lipid bilayer. Our studies illuminate general mechanisms for substrate recognition and catalysis in the UbiA superfamily and rationalize disease-related mutations in humans.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxybenzoate octaprenyltransferase
A, B, C, D, E
A, B, C, D, E, F
303Aeropyrum pernix K1Mutation(s): 0 
Gene Names: ubiAAPE_1570
EC: 2.5.1
Membrane Entity: Yes 
Find proteins for Q9YBM8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YBM8 
Go to UniProtKB:  Q9YBM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YBM8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.09α = 90
b = 123.07β = 90
c = 423.48γ = 90
Software Package:
Software NamePurpose
RAPDdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references