6IBO

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability.

Pravata, V.M.Muha, V.Gundogdu, M.Ferenbach, A.T.Kakade, P.S.Vandadi, V.Wilmes, A.C.Borodkin, V.S.Joss, S.Stavridis, M.P.van Aalten, D.M.F.

(2019) Proc.Natl.Acad.Sci.USA 116: 14961-14970

  • DOI: 10.1073/pnas.1900065116

  • PubMed Abstract: 
  • O-GlcNAc transferase (OGT) is an X-linked gene product that is essential for normal development of the vertebrate embryo. It catalyses the O-GlcNAc posttranslational modification of nucleocytoplasmic proteins and proteolytic maturation of the transcr ...

    O-GlcNAc transferase (OGT) is an X-linked gene product that is essential for normal development of the vertebrate embryo. It catalyses the O-GlcNAc posttranslational modification of nucleocytoplasmic proteins and proteolytic maturation of the transcriptional coregulator Host cell factor 1 (HCF1). Recent studies have suggested that conservative missense mutations distal to the OGT catalytic domain lead to X-linked intellectual disability in boys, but it is not clear if this is through changes in the O-GlcNAc proteome, loss of protein-protein interactions, or misprocessing of HCF1. Here, we report an OGT catalytic domain missense mutation in monozygotic female twins (c. X:70779215 T > A, p. N567K) with intellectual disability that allows dissection of these effects. The patients show limited IQ with developmental delay and skewed X-inactivation. Molecular analyses revealed decreased OGT stability and disruption of the substrate binding site, resulting in loss of catalytic activity. Editing this mutation into the Drosophila genome results in global changes in the O-GlcNAc proteome, while in mouse embryonic stem cells it leads to loss of O-GlcNAcase and delayed differentiation down the neuronal lineage. These data imply that catalytic deficiency of OGT could contribute to X-linked intellectual disability.


    Organizational Affiliation

    Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom; dmfvanaalten@dundee.ac.uk.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom.,Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom.,West of Scotland Genetic Service, Queen Elizabeth University Hospital, G51 4TF Glasgow, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
A
723Homo sapiensMutation(s): 0 
Gene Names: OGT
EC: 2.4.1.255
Find proteins for O15294 (Homo sapiens)
Go to Gene View: OGT
Go to UniProtKB:  O15294
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-VAL-SER-ARG-ALA
C
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
12V
Query on 12V

Download SDF File 
Download CCD File 
A
(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE
C17 H27 N3 O16 P2 S
JPRVHSQHWXZSNC-UBDZBXRQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.201 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 137.737α = 90.00
b = 150.617β = 90.00
c = 199.996γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom110061

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references