5BNW

The active site of O-GlcNAc transferase imposes constraints on substrate sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The active site of O-GlcNAc transferase imposes constraints on substrate sequence.

Pathak, S.Alonso, J.Schimpl, M.Rafie, K.Blair, D.E.Borodkin, V.S.Schuttelkopf, A.W.Albarbarawi, O.van Aalten, D.M.

(2015) Nat Struct Mol Biol 22: 744-750

  • DOI: https://doi.org/10.1038/nsmb.3063
  • Primary Citation of Related Structures:  
    4XI9, 4XIF, 5BNW, 5C1D

  • PubMed Abstract: 

    O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoans. Although this enzyme modifies hundreds of proteins with O-GlcNAc, it is not understood how OGT achieves substrate specificity. In this study, we describe the application of a high-throughput OGT assay to a library of peptides. We mapped sites of O-GlcNAc modification by electron transfer dissociation MS and found that they correlate with previously detected O-GlcNAc sites. Crystal structures of four acceptor peptides in complex with Homo sapiens OGT suggest that a combination of size and conformational restriction defines sequence specificity in the -3 to +2 subsites. This work reveals that although the N-terminal TPR repeats of OGT may have roles in substrate recognition, the sequence restriction imposed by the peptide-binding site makes a substantial contribution to O-GlcNAc site specificity.


  • Organizational Affiliation

    MRC Protein Phosphorylation and Ubiquitylation Unit and College of Life Sciences, University of Dundee, Dundee, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit723Homo sapiensMutation(s): 0 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15294
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
laminB1 residues 179-191B [auth D]13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03252 (Homo sapiens)
Explore Q03252 
Go to UniProtKB:  Q03252
PHAROS:  Q03252
GTEx:  ENSG00000176619 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03252
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
12V
Query on 12V

Download Ideal Coordinates CCD File 
C [auth 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
C17 H27 N3 O16 P2 S
JPRVHSQHWXZSNC-UBDZBXRQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.183α = 90
b = 150.176β = 90
c = 199.241γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT087590MA

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-09-16
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description