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

Research output: Contribution to journalArticle

13 Citations (Scopus)

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 a-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-b3-GlcNAc-b4-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-b3-GlcNAc-b4-Man is recognized by a surface groove, and the GalNAc-b3-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.

Original languageEnglish (US)
Article numbere22238
JournaleLife
Volume5
Issue numberNOVEMBER2016
DOIs
StatePublished - Nov 23 2016

Fingerprint

Mannose
Catalytic Domain
Phosphotransferases
Proteins
Polysaccharides
Zebrafish Proteins
Dystroglycans
Trisaccharides
Phosphorylation
Biosynthesis
Laminin
Mutant Proteins
Disulfides
Adenosine Diphosphate
Crystal structure
Ions
Substrates

ASJC Scopus subject areas

  • Neuroscience(all)
  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Zhu, Q., Venzke, D., Walimbe, A. S., Anderson, M. E., Fu, Q., Kinch, L. N., ... Xiao, J. (2016). Structure of protein O-mannose kinase reveals a unique active site architecture. eLife, 5(NOVEMBER2016), [e22238]. https://doi.org/10.7554/eLife.22238

Structure of protein O-mannose kinase reveals a unique active site architecture. / Zhu, Qinyu; Venzke, David; Walimbe, Ameya S.; Anderson, Mary E.; Fu, Qiuyu; Kinch, Lisa N.; Wang, Wei; Chen, Xing; Grishin, Nick V.; Huang, Niu; Yu, Liping; Dixon, Jack E.; Campbell, Kevin P.; Xiao, Junyu.

In: eLife, Vol. 5, No. NOVEMBER2016, e22238, 23.11.2016.

Research output: Contribution to journalArticle

Zhu, Q, Venzke, D, Walimbe, AS, Anderson, ME, Fu, Q, Kinch, LN, Wang, W, Chen, X, Grishin, NV, Huang, N, Yu, L, Dixon, JE, Campbell, KP & Xiao, J 2016, 'Structure of protein O-mannose kinase reveals a unique active site architecture', eLife, vol. 5, no. NOVEMBER2016, e22238. https://doi.org/10.7554/eLife.22238
Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN et al. Structure of protein O-mannose kinase reveals a unique active site architecture. eLife. 2016 Nov 23;5(NOVEMBER2016). e22238. https://doi.org/10.7554/eLife.22238
Zhu, Qinyu ; Venzke, David ; Walimbe, Ameya S. ; Anderson, Mary E. ; Fu, Qiuyu ; Kinch, Lisa N. ; Wang, Wei ; Chen, Xing ; Grishin, Nick V. ; Huang, Niu ; Yu, Liping ; Dixon, Jack E. ; Campbell, Kevin P. ; Xiao, Junyu. / Structure of protein O-mannose kinase reveals a unique active site architecture. In: eLife. 2016 ; Vol. 5, No. NOVEMBER2016.
@article{11856938bf424c3395d9bfa619bf5e01,
title = "Structure of protein O-mannose kinase reveals a unique active site architecture",
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 a-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-b3-GlcNAc-b4-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-b3-GlcNAc-b4-Man is recognized by a surface groove, and the GalNAc-b3-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.",
author = "Qinyu Zhu and David Venzke and Walimbe, {Ameya S.} and Anderson, {Mary E.} and Qiuyu Fu and Kinch, {Lisa N.} and Wei Wang and Xing Chen and Grishin, {Nick V.} and Niu Huang and Liping Yu and Dixon, {Jack E.} and Campbell, {Kevin P.} and Junyu Xiao",
year = "2016",
month = "11",
day = "23",
doi = "10.7554/eLife.22238",
language = "English (US)",
volume = "5",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
number = "NOVEMBER2016",

}

TY - JOUR

T1 - Structure of protein O-mannose kinase reveals a unique active site architecture

AU - Zhu, Qinyu

AU - Venzke, David

AU - Walimbe, Ameya S.

AU - Anderson, Mary E.

AU - Fu, Qiuyu

AU - Kinch, Lisa N.

AU - Wang, Wei

AU - Chen, Xing

AU - Grishin, Nick V.

AU - Huang, Niu

AU - Yu, Liping

AU - Dixon, Jack E.

AU - Campbell, Kevin P.

AU - Xiao, Junyu

PY - 2016/11/23

Y1 - 2016/11/23

N2 - The ‘pseudokinase’ SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on a-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-b3-GlcNAc-b4-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-b3-GlcNAc-b4-Man is recognized by a surface groove, and the GalNAc-b3-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.

AB - The ‘pseudokinase’ SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on a-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-b3-GlcNAc-b4-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-b3-GlcNAc-b4-Man is recognized by a surface groove, and the GalNAc-b3-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.

UR - http://www.scopus.com/inward/record.url?scp=85005966799&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85005966799&partnerID=8YFLogxK

U2 - 10.7554/eLife.22238

DO - 10.7554/eLife.22238

M3 - Article

C2 - 27879205

AN - SCOPUS:85005966799

VL - 5

JO - eLife

JF - eLife

SN - 2050-084X

IS - NOVEMBER2016

M1 - e22238

ER -