6EOU

O-GlcNAc transferase TPR domain with the intellectual disability associated mutation L254F

• PDB DOI: https://doi.org/10.2210/pdb6EOU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-10-10 Released: 2018-05-09 
• Deposition Author(s): Gundogdu, M., van Aalten, D.M.F.
• Funding Organization(s): Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.227 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix.

Gundogdu, M., Llabres, S., Gorelik, A., Ferenbach, A.T., Zachariae, U., van Aalten, D.M.F.

(2018) Cell Chem Biol 25: 513-518.e4

• PubMed: 29606577 
• DOI: https://doi.org/10.1016/j.chembiol.2018.03.004
• Primary Citation of Related Structures:  
  6EOU


• PubMed Abstract: 
  

  O-linked β-N-acetyl- _D -glucosamine (O-GlcNAc) transferase (OGT) regulates protein O-GlcNAcylation, an essential post-translational modification that is abundant in the brain. Recently, OGT mutations have been associated with intellectual disability, although it is not understood how they affect OGT structure and function. Using a multi-disciplinary approach we show that the L254F OGT mutation leads to conformational changes of the tetratricopeptide repeats and reduced activity, revealing the molecular mechanisms contributing to pathogenesis.

---

Organizational Affiliation: 

Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5HE, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.54 kDa 
• Atom Count: 2,988 
• Modelled Residue Count: 343 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A	388	Homo sapiens	Mutation(s): 1  Gene Names: OGT EC: 2.4.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens) Explore O15294  Go to UniProtKB:  O15294
PHAROS:  O15294 GTEx:  ENSG00000147162

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.227 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45	α = 90
b = 203.162	β = 90
c = 116.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Gundogdu, M., van Aalten, D.M.F.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	110061

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references
• Version 1.2: 2018-07-11
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description