4XI9

Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RBL2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb.3063
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
A, B, C, D
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
Retinoblastoma-like protein 2
E, F, G, H
8Homo sapiensMutation(s): 0 
Gene Names: RBL2 (RB2)
Find proteins for Q08999 (Homo sapiens)
Go to Gene View: RBL2
Go to UniProtKB:  Q08999
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
12V
Query on 12V

Download SDF File 
Download CCD File 
A, B, C, D
(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: 3.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 273.910α = 90.00
b = 273.910β = 90.00
c = 142.930γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT087590MA

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2015-09-16
    Type: Database references