Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 134.15 kDa 
• Atom Count: 9589 
• Residue Count: 1170 
• Unique protein chains: 1

2CBJ

Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase in complex with PUGNAc

• DOI: 10.2210/pdb2CBJ/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-05 Released: 2006-02-13 
• Deposition Author(s): Rao, F.V., Dorfmueller, H.C., Villa, F., Allwood, M., Eggleston, I.M., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis.

Rao, F.V., Dorfmueller, H.C., Villa, F., Allwood, M., Eggleston, I.M., van Aalten, D.M.

(2006) EMBO J 25: 1569-1578

• PubMed: 16541109 
• DOI: 10.1038/sj.emboj.7601026
• Primary Citation of Related Structures:  
  2CBJ, 2CBI


• PubMed Abstract: 
  

O-linked N-acetylglucosamine (O-GlcNAc) modification of specific serines/threonines on intracellular proteins in higher eukaryotes has been shown to directly regulate important processes such as the cell cycle, insulin sensitivity and transcription. The structure, molecular mechanisms of catalysis, protein substrate recognition/specificity of the eukaryotic O-GlcNAc transferase and hydrolase are largely unknown. Here we describe the crystal structure, enzymology and in vitro activity on human substrates of Clostridium perfringens NagJ, a close homologue of human O-GlcNAcase (OGA), representing the first family 84 glycoside hydrolase structure. The structure reveals a deep active site pocket highly conserved with the human enzyme, compatible with binding of O-GlcNAcylated peptides. Together with mutagenesis data, the structure supports a variant of the substrate-assisted catalytic mechanism, involving two aspartic acids and an unusually positioned tyrosine. Insights into recognition of substrate come from a complex with the transition state mimic O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (Ki=5.4 nM). Strikingly, the enzyme is inhibited by the pseudosubstrate peptide Ala-Cys(-S-GlcNAc)-Ala, and has OGA activity against O-GlcNAcylated human proteins, suggesting that the enzyme is a suitable model for further studies into the function of human OGA.

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Organizational Affiliation: 

Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYALURONIDASE	A, B	594	Clostridium perfringens	Mutation(s): 0  EC: 3.2.1.35 (PDB Primary Data), 3.2.1.169 (UniProt)
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore Q0TR53  Go to UniProtKB:  Q0TR53

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAN	A, B	O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE C15 H19 N3 O7 PBLNJFVQMUMOJY-JXZOILRNSA-N
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
OAN	Ki:  5.400000095367432   nM  Binding MOAD
OAN	Ki :  5.400000095367432   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.613	α = 90
b = 145.745	β = 90
c = 152.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-05 
• Released Date: 2006-02-13 
Deposition Author(s): Rao, F.V., Dorfmueller, H.C., Villa, F., Allwood, M., Eggleston, I.M., van Aalten, D.M.F.

Revision History 

• Version 1.0: 2006-02-13
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Non-polymer description, Other, Refinement description, Version format compliance
• Version 1.2: 2017-07-05
  Changes: Data collection
• Version 1.3: 2018-02-28
  Changes: Database references, Source and taxonomy