UbiJ-SCP2 Ubiquinone synthesis protein

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone.

Hajj Chehade, M.Pelosi, L.Fyfe, C.D.Loiseau, L.Rascalou, B.Brugiere, S.Kazemzadeh, K.Vo, C.D.Ciccone, L.Aussel, L.Coute, Y.Fontecave, M.Barras, F.Lombard, M.Pierrel, F.

(2019) Cell Chem Biol 26: 482-492.e7

  • DOI: https://doi.org/10.1016/j.chembiol.2018.12.001
  • Primary Citation of Related Structures:  
    6H6N, 6H6O, 6H6P

  • PubMed Abstract: 

    Ubiquinone (UQ) is a polyprenylated lipid that is conserved from bacteria to humans and is crucial to cellular respiration. How the cell orchestrates the efficient synthesis of UQ, which involves the modification of extremely hydrophobic substrates by multiple sequential enzymes, remains an unresolved issue. Here, we demonstrate that seven Ubi proteins form the Ubi complex, a stable metabolon that catalyzes the last six reactions of the UQ biosynthetic pathway in Escherichia coli. The SCP2 domain of UbiJ forms an extended hydrophobic cavity that binds UQ intermediates inside the 1-MDa Ubi complex. We purify the Ubi complex from cytoplasmic extracts and demonstrate that UQ biosynthesis occurs in this fraction, challenging the current thinking of a membrane-associated biosynthetic process. Collectively, our results document a rare case of stable metabolon and highlight how the supramolecular organization of soluble enzymes allows the modification of hydrophobic substrates in a hydrophilic environment.

  • Organizational Affiliation

    Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinone biosynthesis protein UbiJ
A, B
131Escherichia coli K-12Mutation(s): 0 
Gene Names: ubiJyigPb3834JW3811
Find proteins for P0ADP7 (Escherichia coli (strain K12))
Explore P0ADP7 
Go to UniProtKB:  P0ADP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADP7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.3α = 90
b = 67.93β = 90
c = 73.08γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations