5GZ9

Crystal structure of catalytic domain of Protein O-mannosyl Kinase in complexes with AMP-PNP, Magnesium ions and glycopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy.

Nagae, M.Mishra, S.K.Neyazaki, M.Oi, R.Ikeda, A.Matsugaki, N.Akashi, S.Manya, H.Mizuno, M.Yagi, H.Kato, K.Senda, T.Endo, T.Nogi, T.Yamaguchi, Y.

(2017) Genes Cells 22: 348-359

  • DOI: 10.1111/gtc.12480
  • Primary Citation of Related Structures:  
    5GZ9, 5GZ8

  • PubMed Abstract: 
  • Orchestration of the multiple enzymes engaged in O-mannose glycan synthesis provides a matriglycan on α-dystroglycan (α-DG) which attracts extracellular matrix (ECM) proteins such as laminin. Aberrant O-mannosylation of α-DG leads to severe congenital muscular dystrophies due to detachment of ECM proteins from the basal membrane ...

    Orchestration of the multiple enzymes engaged in O-mannose glycan synthesis provides a matriglycan on α-dystroglycan (α-DG) which attracts extracellular matrix (ECM) proteins such as laminin. Aberrant O-mannosylation of α-DG leads to severe congenital muscular dystrophies due to detachment of ECM proteins from the basal membrane. Phosphorylation at C6-position of O-mannose catalyzed by protein O-mannosyl kinase (POMK) is a crucial step in the biosynthetic pathway of O-mannose glycan. Several mis-sense mutations of the POMK catalytic domain are known to cause a severe congenital muscular dystrophy, Walker-Warburg syndrome. Due to the low sequence similarity with other typical kinases, structure-activity relationships of this enzyme remain unclear. Here, we report the crystal structures of the POMK catalytic domain in the absence and presence of an ATP analogue and O-mannosylated glycopeptide. The POMK catalytic domain shows a typical protein kinase fold consisting of N- and C-lobes. Mannose residue binds to POMK mainly via the hydroxyl group at C2-position, differentiating from other monosaccharide residues. Intriguingly, the two amino acid residues K92 and D228, interacting with the triphosphate group of ATP, are donated from atypical positions in the primary structure. Mutations in this protein causing muscular dystrophies can now be rationalized.


    Organizational Affiliation

    Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein O-mannose kinaseA305Mus musculusMutation(s): 2 
Gene Names: PomkSgk196
EC: 2.7.1 (PDB Primary Data), 2.7.1.183 (UniProt)
UniProt
Find proteins for Q3TUA9 (Mus musculus)
Explore Q3TUA9 
Go to UniProtKB:  Q3TUA9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
E [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.32α = 90
b = 81.32β = 90
c = 146.838γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan15K18496
MEXTJapan26110724

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary