Structure of protein O-mannose kinase reveals a unique active site architecture
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 Dan...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2016-11-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/22238 |
| _version_ | 1828375091649445888 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Qinyu Zhu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T07:41:52Z |
| format | Article |
| id | doaj.art-eec560f670404fffbe2ea90fd70ef501 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:41:52Z |
| publishDate | 2016-11-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-eec560f670404fffbe2ea90fd70ef5012022-12-22T02:05:28ZengeLife Sciences Publications LtdeLife2050-084X2016-11-01510.7554/eLife.22238Structure of protein O-mannose kinase reveals a unique active site architectureQinyu Zhu0David Venzke1Ameya S Walimbe2Mary E Anderson3Qiuyu Fu4Lisa N Kinch5Wei Wang6Xing Chen7Nick V Grishin8Niu Huang9Liping Yu10Jack E Dixon11Kevin P Campbell12https://orcid.org/0000-0003-2066-5889Junyu Xiao13https://orcid.org/0000-0003-1822-1701The 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, ChinaDepartment 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 StatesDepartment 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 StatesDepartment 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 StatesNational Institute of Biological Sciences, Beijing, ChinaDepartment of Biophysics, University of Texas Southwestern Medical Center, Dallas, United StatesAcademy 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, ChinaAcademy 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, ChinaDepartment of Biophysics, University of Texas Southwestern Medical Center, Dallas, United StatesNational Institute of Biological Sciences, Beijing, ChinaMedical Nuclear Magnetic Resonance Facility, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United StatesDepartment 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 StatesDepartment 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 StatesThe 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, ChinaThe ‘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.https://elifesciences.org/articles/22238muscular dystrophydystroglycan biosynthesissecretory pathway kinase |
| spellingShingle | 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 Structure of protein O-mannose kinase reveals a unique active site architecture eLife muscular dystrophy dystroglycan biosynthesis secretory pathway kinase |
| title | Structure of protein O-mannose kinase reveals a unique active site architecture |
| title_full | Structure of protein O-mannose kinase reveals a unique active site architecture |
| title_fullStr | Structure of protein O-mannose kinase reveals a unique active site architecture |
| title_full_unstemmed | Structure of protein O-mannose kinase reveals a unique active site architecture |
| title_short | Structure of protein O-mannose kinase reveals a unique active site architecture |
| title_sort | structure of protein o mannose kinase reveals a unique active site architecture |
| topic | muscular dystrophy dystroglycan biosynthesis secretory pathway kinase |
| url | https://elifesciences.org/articles/22238 |
| work_keys_str_mv | AT qinyuzhu structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT davidvenzke structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT ameyaswalimbe structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT maryeanderson structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT qiuyufu structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT lisankinch structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT weiwang structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT xingchen structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT nickvgrishin structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT niuhuang structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT lipingyu structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT jackedixon structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT kevinpcampbell structureofproteinomannosekinaserevealsauniqueactivesitearchitecture AT junyuxiao structureofproteinomannosekinaserevealsauniqueactivesitearchitecture |