Structure of protein O-mannose kinase reveals a unique active site architecture
Qinyu Zhu,
David Venzke,
Ameya S Walimbe,
Mary E Anderson,
Qiuyu Fu,
Lisa N Kinch,
Wei Wang,
Xing Chen,
Nick V Grishin,
Niu Huang,
Liping Yu,
Jack E Dixon,
Kevin P Campbell,
Junyu Xiao
Affiliations
Qinyu Zhu
The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China; Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
David Venzke
Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States; Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States; Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
Ameya S Walimbe
Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States; Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States; Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
Mary E Anderson
Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States; Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States; Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
Qiuyu Fu
National Institute of Biological Sciences, Beijing, China
Lisa N Kinch
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
Wei Wang
Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
Xing Chen
Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
Nick V Grishin
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
Niu Huang
National Institute of Biological Sciences, Beijing, China
Liping Yu
Medical Nuclear Magnetic Resonance Facility, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
Jack E Dixon
Department of Pharmacology, University of California, San Diego, La Jolla, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States
Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States; Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States; Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China; Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
The ‘pseudokinase’ SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on α-dystroglycan. However, the catalytic mechanism underlying this activity remains elusive. Here we present the crystal structure of Danio rerio POMK in complex with Mg2+ ions, ADP, aluminum fluoride, and the GalNAc-β3-GlcNAc-β4-Man trisaccharide substrate, thereby providing a snapshot of the catalytic transition state of this unusual kinase. The active site of POMK is established by residues located in non-canonical positions and is stabilized by a disulfide bridge. GalNAc-β3-GlcNAc-β4-Man is recognized by a surface groove, and the GalNAc-β3-GlcNAc moiety mediates the majority of interactions with POMK. Expression of various POMK mutants in POMK knockout cells further validated the functional requirements of critical residues. Our results provide important insights into the ability of POMK to function specifically as a glycan kinase, and highlight the structural diversity of the human kinome.
