5GGI | pdb_00005ggi

Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.238 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1073/pnas.1525545113
  • Primary Citation Related Structures: 
    5GGF, 5GGG, 5GGI, 5GGJ, 5GGK, 5GGL, 5GGN, 5GGO, 5GGP

  • 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 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;

Macromolecule Content 

  • Total Structure Weight: 134.11 kDa 
  • Atom Count: 7,946 
  • Modeled Residue Count: 960 
  • Deposited Residue Count: 1,178 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
A, B
578Homo sapiensMutation(s): 1 
Gene Names: POMGNT1MGAT1.2UNQ746/PRO1475
EC: 2.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WZA1 (Homo sapiens)
Explore Q8WZA1 
Go to UniProtKB:  Q8WZA1
PHAROS:  Q8WZA1
GTEx:  ENSG00000085998 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WZA1
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mannosyl-peptideC [auth F],
D [auth G]
11Homo sapiensMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP

Query on UDP



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
J [auth F],
K [auth G]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN

Query on MN



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.238 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.162α = 90
b = 126.539β = 90
c = 172.865γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan26840029
JSPSJapan16K07284

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-03-20
    Changes: Source and taxonomy
  • Version 1.6: 2024-10-23
    Changes: Structure summary