4OD4

Apo structure of a UbiA homolog from Aeropyrum pernix K1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.301 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into ubiquinone biosynthesis in membranes.

Cheng, W.Li, W.

(2014) Science 343: 878-881

  • DOI: 10.1126/science.1246774
  • Primary Citation of Related Structures:  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 cardiovascul ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxybenzoate octaprenyltransferase
A, B, C, D, E, F
303Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)Gene Names: ubiA
EC: 2.5.1.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
UbiA Prenyltransferases
Protein: 
UbiA homolog with bound substrate
Find proteins for Q9YBM8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Go to UniProtKB:  Q9YBM8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.301 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.272 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.090α = 90.00
b = 123.070β = 90.00
c = 423.480γ = 90.00
Software Package:
Software NamePurpose
RAPDdata collection
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-09 
  • Released Date: 2014-03-19 
  • Deposition Author(s): Li, W., Cheng, W.

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release