5I35

Structure of the Human mitochondrial kinase COQ8A R611K with AMPPNP (Cerebellar Ataxia and Ubiquinone Deficiency Through Loss of Unorthodox Kinase Activity)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity.

Stefely, J.A.Licitra, F.Laredj, L.Reidenbach, A.G.Kemmerer, Z.A.Grangeray, A.Jaeg-Ehret, T.Minogue, C.E.Ulbrich, A.Hutchins, P.D.Wilkerson, E.M.Ruan, Z.Aydin, D.Hebert, A.S.Guo, X.Freiberger, E.C.Reutenauer, L.Jochem, A.Chergova, M.Johnson, I.E.Lohman, D.C.Rush, M.J.Kwiecien, N.W.Singh, P.K.Schlagowski, A.I.Floyd, B.J.Forsman, U.Sindelar, P.J.Westphall, M.S.Pierrel, F.Zoll, J.Dal Peraro, M.Kannan, N.Bingman, C.A.Coon, J.J.Isope, P.Puccio, H.Pagliarini, D.J.

(2016) Mol.Cell 63: 608-620

  • DOI: 10.1016/j.molcel.2016.06.030

  • PubMed Abstract: 
  • The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosy ...

    The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosynthesis and an ataxia (ARCA2) through unclear means. We show that mice lacking COQ8A develop a slowly progressive cerebellar ataxia linked to Purkinje cell dysfunction and mild exercise intolerance, recapitulating ARCA2. Interspecies biochemical analyses show that COQ8A and yeast Coq8p specifically stabilize a CoQ biosynthesis complex through unorthodox PKL functions. Although COQ8 was predicted to be a protein kinase, we demonstrate that it lacks canonical protein kinase activity in trans. Instead, COQ8 has ATPase activity and interacts with lipid CoQ intermediates, functions that are likely conserved across all domains of life. Collectively, our results lend insight into the molecular activities of the ancient UbiB family and elucidate the biochemical underpinnings of a human disease.


    Organizational Affiliation

    Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Atypical kinase ADCK3, mitochondrial
A
393Homo sapiensMutation(s): 1 
Gene Names: COQ8A (ADCK3, CABC1)
EC: 2.7.-.-
Find proteins for Q8NI60 (Homo sapiens)
Go to Gene View: COQ8A
Go to UniProtKB:  Q8NI60
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.050α = 90.00
b = 59.120β = 97.69
c = 51.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU01GM094622
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM112057-02

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-08-24
    Type: Database references
  • Version 1.2: 2016-08-31
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence