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

doi:10.7554/eLife.22238

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Structure of protein O-mannose kinase reveals a unique active site architecture

Journal article

Open access

Peer reviewed

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, …

eLife, Vol.5, e22238

11/23/2016

DOI: 10.7554/eLife.22238

PMCID: PMC5142810

PMID: 27879205

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Abstract

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 POMK in complex with Mg 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 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.

Gene Expression

Mutation

Phosphorylation

Protein Kinases - metabolism

Protein Kinases - genetics

Baculoviridae - metabolism

Humans

Dystroglycans - metabolism

Protein Kinases - chemistry

Substrate Specificity

Baculoviridae - genetics

Crystallography, X-Ray

Adenosine Diphosphate - chemistry

Fish Proteins - genetics

Mannose - metabolism

Fluorides - chemistry

Sf9 Cells

Trisaccharides - chemistry

Aluminum Compounds - chemistry

Cloning, Molecular

Dystroglycans - chemistry

Protein Interaction Domains and Motifs

Trisaccharides - metabolism

Mannose - chemistry

Recombinant Proteins - metabolism

Amino Acid Sequence

Protein Conformation, alpha-Helical

Catalytic Domain

Fish Proteins - chemistry

Fish Proteins - metabolism

Models, Molecular

Recombinant Proteins - chemistry

Magnesium - metabolism

Recombinant Proteins - genetics

Sequence Homology, Amino Acid

Magnesium - chemistry

Sequence Alignment

Animals

Protein Conformation, beta-Strand

Zebrafish - metabolism

Protein Binding

Adenosine Diphosphate - metabolism

Details

Title: Subtitle: Structure of protein O-mannose kinase reveals a unique active site architecture
Creators: Qinyu Zhu - Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
David Venzke - Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
Ameya S Walimbe - Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
Mary E Anderson - 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 - Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
Xing Chen - 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 Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States
Kevin P Campbell - Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
Junyu Xiao - Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
Resource Type: Journal article
Publication Details: eLife, Vol.5, e22238
DOI: 10.7554/eLife.22238
PMID: 27879205
PMCID: PMC5142810
NLM abbreviation: Elife
ISSN: 2050-084X
eISSN: 2050-084X
Publisher: England
Grant note: R01 GM094575 / NIGMS NIH HHS U54 NS053672 / NINDS NIH HHS R01 DK018024 / NIDDK NIH HHS
Language: English
Date published: 11/23/2016
Academic Unit: Neurology; Molecular Physiology and Biophysics; Iowa Neuroscience Institute; Biochemistry and Molecular Biology; Medicine Administration
Record Identifier: 9984020505902771

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