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: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.5 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
  • Primary Citation of Related Structures:  
    5I35

  • 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) biosynthesis and an ataxia (ARCA2) through unclear means ...

    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. Electronic address: dpagliarini@morgridge.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Atypical kinase ADCK3, mitochondrialA393Homo sapiensMutation(s): 1 
Gene Names: ADCK3CABC1PP265COQ8A
EC: 2.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NI60 (Homo sapiens)
Explore Q8NI60 
Go to UniProtKB:  Q8NI60
PHAROS:  Q8NI60
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
B [auth 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
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.05α = 90
b = 59.12β = 97.69
c = 51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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 StatesU01GM094622
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM112057-02

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-08-31
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence