4PED

Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis.

Stefely, J.A.Reidenbach, A.G.Ulbrich, A.Oruganty, K.Floyd, B.J.Jochem, A.Saunders, J.M.Johnson, I.E.Minogue, C.E.Wrobel, R.L.Barber, G.E.Lee, D.Li, S.Kannan, N.Coon, J.J.Bingman, C.A.Pagliarini, D.J.

(2015) Mol.Cell 57: 83-94

  • DOI: 10.1016/j.molcel.2014.11.002

  • PubMed Abstract: 
  • The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. Here, we quantitatively define UbiB-spec ...

    The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. Here, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flips this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperone activity of bc1 complex-like, mitochondrial
A
393Homo sapiensMutation(s): 0 
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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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: 1.64 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.671α = 90.00
b = 54.557β = 94.00
c = 45.009γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
ARPmodel building
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

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

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-01-21
    Type: Database references
  • Version 1.3: 2015-02-04
    Type: Derived calculations
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy