protein O-mannose kinase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 

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This is version 2.0 of the entry. See complete history


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

Zhu, Q.Venzke, D.Walimbe, A.S.Anderson, M.E.Fu, Q.Kinch, L.N.Wang, W.Chen, X.Grishin, N.V.Huang, N.Yu, L.Dixon, J.E.Campbell, K.P.Xiao, J.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.22238
  • Primary Citation of Related Structures:  

  • PubMed 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 Danio rerio POMK in complex with Mg 2+ 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.

  • Organizational Affiliation

    The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein O-mannose kinase290Danio rerioMutation(s): 0 
Gene Names: pomksgk196
Find proteins for Q5U3W1 (Danio rerio)
Explore Q5U3W1 
Go to UniProtKB:  Q5U3W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5U3W1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G82715NG
GlyCosmos:  G82715NG
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.55α = 90
b = 70.55β = 90
c = 66.935γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2016-12-07 
  • Deposition Author(s): Xiao, J.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary