4RHP

Crystal structure of human COQ9 in complex with a phospholipid, Northeast Structural Genomics Consortium Target HR5043


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.393 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis.

Lohman, D.C.Forouhar, F.Beebe, E.T.Stefely, M.S.Minogue, C.E.Ulbrich, A.Stefely, J.A.Sukumar, S.Luna-Sanchez, M.Jochem, A.Lew, S.Seetharaman, J.Xiao, R.Wang, H.Westphall, M.S.Wrobel, R.L.Everett, J.K.Mitchell, J.C.Lopez, L.C.Coon, J.J.Tong, L.Pagliarini, D.J.

(2014) Proc.Natl.Acad.Sci.USA 111: E4697-E4705

  • DOI: 10.1073/pnas.1413128111

  • PubMed Abstract: 
  • Coenzyme Q (CoQ) is an isoprenylated quinone that is essential for cellular respiration and is synthesized in mitochondria by the combined action of at least nine proteins (COQ1-9). Although most COQ proteins are known to catalyze modifications to Co ...

    Coenzyme Q (CoQ) is an isoprenylated quinone that is essential for cellular respiration and is synthesized in mitochondria by the combined action of at least nine proteins (COQ1-9). Although most COQ proteins are known to catalyze modifications to CoQ precursors, the biochemical role of COQ9 remains unclear. Here, we report that a disease-related COQ9 mutation leads to extensive disruption of the CoQ protein biosynthetic complex in a mouse model, and that COQ9 specifically interacts with COQ7 through a series of conserved residues. Toward understanding how COQ9 can perform these functions, we solved the crystal structure of Homo sapiens COQ9 at 2.4 Å. Unexpectedly, our structure reveals that COQ9 has structural homology to the TFR family of bacterial transcriptional regulators, but that it adopts an atypical TFR dimer orientation and is not predicted to bind DNA. Our structure also reveals a lipid-binding site, and mass spectrometry-based analyses of purified COQ9 demonstrate that it associates with multiple lipid species, including CoQ itself. The conserved COQ9 residues necessary for its interaction with COQ7 comprise a surface patch around the lipid-binding site, suggesting that COQ9 might serve to present its bound lipid to COQ7. Collectively, our data define COQ9 as the first, to our knowledge, mammalian TFR structural homolog and suggest that its lipid-binding capacity and association with COQ7 are key features for enabling CoQ biosynthesis.


    Organizational Affiliation

    Departments of Biochemistry.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinone biosynthesis protein COQ9, mitochondrial
A, B
235Homo sapiensGene Names: COQ9 (C16orf49)
Find proteins for O75208 (Homo sapiens)
Go to Gene View: COQ9
Go to UniProtKB:  O75208
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEF
Query on PEF

Download SDF File 
Download CCD File 
A
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.393 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.340α = 90.00
b = 97.628β = 95.77
c = 64.109γ = 90.00
Software Package:
Software NamePurpose
RESOLVEmodel building
ADSCdata collection
XTALVIEWrefinement
SnBphasing
RESOLVEphasing
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references
  • Version 1.2: 2014-11-19
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description