5GGF

Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan

Kuwabara, N.Manya, H.Yamada, T.Tateno, H.Kanagawa, M.Kobayashi, K.Akasaka-Manya, K.Hirose, Y.Mizuno, M.Ikeguchi, M.Toda, T.Hirabayashi, J.Senda, T.Endo, T.Kato, R.

(2016) Proc Natl Acad Sci U S A 113: 9280-9285

  • DOI: 10.1073/pnas.1525545113
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The dystrophin glycoprotein complex, which connects the cell membrane to the basement membrane, is essential for a variety of biological events, including maintenance of muscle integrity. An O-mannose-type GalNAc-β1,3-GlcNAc-β1,4-(phosphate-6)-Man st ...

    The dystrophin glycoprotein complex, which connects the cell membrane to the basement membrane, is essential for a variety of biological events, including maintenance of muscle integrity. An O-mannose-type GalNAc-β1,3-GlcNAc-β1,4-(phosphate-6)-Man structure of α-dystroglycan (α-DG), a subunit of the complex that is anchored to the cell membrane, interacts directly with laminin in the basement membrane. Reduced glycosylation of α-DG is linked to some types of inherited muscular dystrophy; consistent with this relationship, many disease-related mutations have been detected in genes involved in O-mannosyl glycan synthesis. Defects in protein O-linked mannose β1,2-N-acetylglucosaminyltransferase 1 (POMGnT1), a glycosyltransferase that participates in the formation of GlcNAc-β1,2-Man glycan, are causally related to muscle-eye-brain disease (MEB), a congenital muscular dystrophy, although the role of POMGnT1 in postphosphoryl modification of GalNAc-β1,3-GlcNAc-β1,4-(phosphate-6)-Man glycan remains elusive. Our crystal structures of POMGnT1 agreed with our previous results showing that the catalytic domain recognizes substrate O-mannosylated proteins via hydrophobic interactions with little sequence specificity. Unexpectedly, we found that the stem domain recognizes the β-linked GlcNAc of O-mannosyl glycan, an enzymatic product of POMGnT1. This interaction may recruit POMGnT1 to a specific site of α-DG to promote GlcNAc-β1,2-Man clustering and also may recruit other enzymes that interact with POMGnT1, e.g., fukutin, which is required for further modification of the GalNAc-β1,3-GlcNAc-β1,4-(phosphate-6)-Man glycan. On the basis of our findings, we propose a mechanism for the deficiency in postphosphoryl modification of the glycan observed in POMGnT1-KO mice and MEB patients.


    Organizational Affiliation

    Photon Factory, Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan; School of High Energy Accelerator Science, SOKENDAI University, Tsukuba, Ibaraki 305-0801, Japan ryuichi.kato@kek.jp endo@tmig.or.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1A, B, C578Homo sapiensMutation(s): 1 
Gene Names: POMGNT1MGAT1.2UNQ746/PRO1475
EC: 2.4.1
Find proteins for Q8WZA1 (Homo sapiens)
Explore Q8WZA1 
Go to UniProtKB:  Q8WZA1
NIH Common Fund Data Resources
PHAROS  Q8WZA1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.688α = 90
b = 186.444β = 90
c = 143.887γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan26840029
JSPSJapan16K07284

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations