Structure of the C-terminal truncated form of E.Coli C5-hydroxylase UBII involved in ubiquinone (Q8) biosynthesis

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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ubiI, a New Gene in Escherichia coli Coenzyme Q Biosynthesis, Is Involved in Aerobic C5-hydroxylation.

Chehade, M.H.Loiseau, L.Lombard, M.Pecqueur, L.Ismail, A.Smadja, M.Golinelli-Pimpaneau, B.Mellot-Draznieks, C.Hamelin, O.Aussel, L.Kieffer-Jaquinod, S.Labessan, N.Barras, F.Fontecave, M.Pierrel, F.

(2013) J Biol Chem 288: 20085-20092

  • DOI: https://doi.org/10.1074/jbc.M113.480368
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Coenzyme Q (ubiquinone or Q) is a redox-active lipid found in organisms ranging from bacteria to mammals in which it plays a crucial role in energy-generating processes. Q biosynthesis is a complex pathway that involves multiple proteins. In this work, we show that the uncharacterized conserved visC gene is involved in Q biosynthesis in Escherichia coli, and we have renamed it ubiI. Based on genetic and biochemical experiments, we establish that the UbiI protein functions in the C5-hydroxylation reaction. A strain deficient in ubiI has a low level of Q and accumulates a compound derived from the Q biosynthetic pathway, which we purified and characterized. We also demonstrate that UbiI is only implicated in aerobic Q biosynthesis and that an alternative enzyme catalyzes the C5-hydroxylation reaction in the absence of oxygen. We have solved the crystal structure of a truncated form of UbiI. This structure shares many features with the canonical FAD-dependent para-hydroxybenzoate hydroxylase and represents the first structural characterization of a monooxygenase involved in Q biosynthesis. Site-directed mutagenesis confirms that residues of the flavin binding pocket of UbiI are important for activity. With our identification of UbiI, the three monooxygenases necessary for aerobic Q biosynthesis in E. coli are known.

  • Organizational Affiliation

    Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire Chimie et Biologie des Métaux, F-38054 Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VisC
A, B
365Escherichia coli K-12Mutation(s): 0 
Gene Names: visCb2906JW2874
EC: 1
Find proteins for P25535 (Escherichia coli (strain K12))
Explore P25535 
Go to UniProtKB:  P25535
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25535
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
G [auth A]
I [auth A]
J [auth B]
C [auth A],
D [auth A],
G [auth A],
I [auth A],
J [auth B],
M [auth B],
N [auth B]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth A],
K [auth B],
L [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.73α = 90
b = 124.14β = 90
c = 71.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Refinement description
  • Version 1.2: 2013-08-21
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations