6DEW

Structure of human COQ9 protein with bound isoprene.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis.

Lohman, D.C.Aydin, D.Von Bank, H.C.Smith, R.W.Linke, V.Weisenhorn, E.McDevitt, M.T.Hutchins, P.Wilkerson, E.M.Wancewicz, B.Russell, J.Stefely, M.S.Beebe, E.T.Jochem, A.Coon, J.J.Bingman, C.A.Dal Peraro, M.Pagliarini, D.J.

(2019) Mol Cell 73: 763-774.e10

  • DOI: 10.1016/j.molcel.2018.11.033
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally ass ...

    The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associated with the mitochondrial inner membrane. Here, we reveal that this process relies on custom lipid-binding properties of COQ9. We show that COQ9 repurposes the bacterial TetR fold to bind aromatic isoprenes with high specificity, including CoQ intermediates that likely reside entirely within the bilayer. We reveal a process by which COQ9 associates with cardiolipin-rich membranes and warps the membrane surface to access this cargo. Finally, we identify a molecular interface between COQ9 and the hydroxylase COQ7, motivating a model whereby COQ9 presents intermediates directly to CoQ enzymes. Overall, our results provide a mechanism for how a lipid-binding protein might access, select, and deliver specific cargo from a membrane to promote biosynthesis.


    Organizational Affiliation

    Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53715, USA. Electronic address: dpagliarini@morgridge.org.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinone biosynthesis protein COQ9, mitochondrialA, B, C, D, E, F212Homo sapiensMutation(s): 0 
Gene Names: COQ9C16orf49HSPC326PSEC0129
Find proteins for O75208 (Homo sapiens)
Explore O75208 
Go to UniProtKB:  O75208
NIH Common Fund Data Resources
PHAROS  O75208
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N1S
Query on N1S

Download CCD File 
A
(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
C15 H26 O
CRDAMVZIKSXKFV-PVMFERMNSA-N
 Ligand Interaction
FOF
Query on FOF

Download CCD File 
A
(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
C15 H26 O
CRDAMVZIKSXKFV-YFVJMOTDSA-N
 Ligand Interaction
FOH
Query on FOH

Download CCD File 
D
(2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
C15 H26 O
CRDAMVZIKSXKFV-FBXUGWQNSA-N
 Ligand Interaction
64Z
Query on 64Z

Download CCD File 
A, B, D
Geraniol
C10 H18 O
GLZPCOQZEFWAFX-JXMROGBWSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.45α = 90
b = 222.78β = 90
c = 130.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115591
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM112057
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM08349

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 2.0: 2019-03-06
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.0: 2019-05-08
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2020-01-01
    Changes: Author supporting evidence