title: Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis.
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-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.
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Stefely
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Reidenbach
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Arne
authors.initials: A
authors.lastname: Ulbrich
authors.affiliation: Department of Biochemistry, University of Georgia, Athens, GA 30602, USA.
authors.forename: Krishnadev
authors.initials: K
authors.lastname: Oruganty
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Brendan J
authors.initials: BJ
authors.lastname: Floyd
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Jochem
authors.affiliation: Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Jaclyn M
authors.initials: JM
authors.lastname: Saunders
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Isabel E
authors.initials: IE
authors.lastname: Johnson
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Minogue
authors.affiliation: Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Russell L
authors.initials: RL
authors.lastname: Wrobel
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Grant E
authors.initials: GE
authors.lastname: Barber
authors.affiliation: Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA.
authors.forename: David
authors.initials: D
authors.lastname: Lee
authors.affiliation: Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA.
authors.forename: Sheng
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Biochemistry, University of Georgia, Athens, GA 30602, USA.
authors.forename: Natarajan
authors.initials: N
authors.lastname: Kannan
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Craig A
authors.initials: CA
authors.lastname: Bingman
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: pagliarini@wisc.edu.
authors.forename: David J
authors.initials: DJ
authors.lastname: Pagliarini
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006801:Humans; D008928:Mitochondria / Q000737:chemistry* / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D010766:Phosphorylation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000254:growth & development / Q000378:metabolism; D016415:Sequence Alignment; D014451:Ubiquinone / Q000096:biosynthesis / Q000737:chemistry*
chemical_list: C553453:COQ8A protein, human; D024101:Mitochondrial Proteins; D011994:Recombinant Proteins; D014451:Ubiquinone