5UN8

Crystal Structure of human O-GlcNAcase in complex with glycopeptide p53

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structures of human O-GlcNAcase and its complexes reveal a new substrate recognition mode.

Li, B., Li, H., Lu, L., Jiang, J.

(2017) Nat. Struct. Mol. Biol. 24: 362-369

  • DOI: 10.1038/nsmb.3390
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Human O-GlcNAcase (hOGA) is the unique enzyme responsible for the hydrolysis of the O-linked β-N-acetyl glucosamine (O-GlcNAc) modification, an essential protein glycosylation event that modulates the function of numerous cellular proteins in respons ...

    Human O-GlcNAcase (hOGA) is the unique enzyme responsible for the hydrolysis of the O-linked β-N-acetyl glucosamine (O-GlcNAc) modification, an essential protein glycosylation event that modulates the function of numerous cellular proteins in response to nutrients and stress. Here we report crystal structures of a truncated hOGA, which comprises the catalytic and stalk domains, in apo form, in complex with an inhibitor, and in complex with a glycopeptide substrate. We found that hOGA forms an unusual arm-in-arm homodimer in which the catalytic domain of one monomer is covered by the stalk domain of the sister monomer to create a substrate-binding cleft. Notably, the residues on the cleft surface afford extensive interactions with the peptide substrate in a recognition mode that is distinct from that of its bacterial homologs. These structures represent the first model of eukaryotic enzymes in the glycoside hydrolase 84 (GH84) family and provide a crucial starting point for understanding the substrate specificity of hOGA, which regulates a broad range of biological and pathological processes.

    Organizational Affiliation: 

    Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein O-GlcNAcase
A, B, C, D
504Homo sapiensMutation(s): 0 
Gene Names: OGA (HEXC, KIAA0679, MEA5, MGEA5)
EC: 3.2.1.169
Find proteins for O60502 (Homo sapiens)
Go to UniProtKB:  O60502
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P53 peptide
E, F, G, H
11Homo sapiensMutation(s): 0 
Gene Names: TP53 (P53)
Find proteins for P04637 (Homo sapiens)
Go to Gene View: TP53
Go to UniProtKB:  P04637
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
E, F, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.909α = 90.00
b = 95.393β = 96.91
c = 149.320γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-30 
  • Released Date: 2017-03-15 
  • Deposition Author(s): Li, B., Jiang, J.
Funding OrganizationLocationGrant Number
University of Wisconsin-MadisonUnited States--

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references
  • Version 1.2: 2017-04-19
    Type: Database references