4K22

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M113.480368

  • 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 wor ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein VisC
A, B
365Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ubiI (visC)
EC: 1.14.13.240
Find proteins for P25535 (Escherichia coli (strain K12))
Go to UniProtKB:  P25535
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.730α = 90.00
b = 124.140β = 90.00
c = 71.890γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Refinement description
  • Version 1.2: 2013-08-21
    Type: Database references