Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 56.83 kDa 
• Atom Count: 4185 
• Modelled Residue Count: 499 
• Deposited Residue Count: 512 
• Unique protein chains: 1

1M01

Wildtype Streptomyces plicatus beta-hexosaminidase in complex with product (GlcNAc)

• PDB DOI: 10.2210/pdb1M01/pdb

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


• Deposited: 2002-06-11 Released: 2003-01-21 
• Deposition Author(s): J Williams, S., Mark, B.L., Vocadlo, D.J., James, M.N.G., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state.

Williams, S.J., Mark, B.L., Vocadlo, D.J., James, M.N., Withers, S.G.

(2002) J Biol Chem 277: 40055-40065

• PubMed: 12171933 
• DOI: 10.1074/jbc.M206481200
• Primary Citation of Related Structures:  
  1M01, 1M03, 1M04


• PubMed Abstract: 
  

SpHex, a retaining family 20 glycosidase from Streptomyces plicatus, catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. Accumulating evidence suggests that the hydrolytic mechanism involves substrate-assisted catalysis wherein the 2-acetamido substituent acts as a nucleophile to form an oxazolinium ion intermediate. The role of a conserved aspartate residue (D313) in the active site of SpHex was investigated through kinetic and structural analyses of two variant enzymes, D313A and D313N. Three-dimensional structures of the wild-type and variant enzymes in product complexes with N-acetyl-d-glucosamine revealed substantial differences. In the D313A variant the 2-acetamido group was found in two conformations of which only one is able to aid in catalysis through anchimeric assistance. The mutation D313N results in a steric clash in the active site between Asn-313 and the 2-acetamido group preventing the 2-acetamido group from providing anchimeric assistance, consistent with the large reduction in catalytic efficiency and the insensitivity of this variant to chemical rescue. By comparison, the D313A mutation results in a shift in a shift in the pH optimum and a modest decrease in activity that can be rescued by using azide as an exogenous nucleophile. These structural and kinetic data provide evidence that Asp-313 stabilizes the transition states flanking the oxazoline intermediate and also assists to correctly orient the 2-acetamido group for catalysis. Based on analogous conserved residues in the family 18 chitinases and family 56 hyaluronidases, the roles played by the Asp-313 residue is likely general for all hexosaminidases using a mechanism involving substrate-assisted catalysis.

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Organizational Affiliation: 

Protein Engineering Network Centres of Excellence of Canada and the Department of Chemistry, University of British Columbia, Vancouver, V6T 1Z1 Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A	512	Streptomyces plicatus	Mutation(s): 0  Gene Names: hex EC: 3.2.1.52
UniProt
Find proteins for O85361 (Streptomyces plicatus) Explore O85361  Go to UniProtKB:  O85361

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
NAG	Binding MOAD:  1M01	Kd: 3.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.276	α = 90
b = 133.276	β = 90
c = 176.204	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-11 
• Released Date: 2003-01-21 
Deposition Author(s): J Williams, S., Mark, B.L., Vocadlo, D.J., James, M.N.G., Withers, S.G.

Revision History  

• Version 1.0: 2003-01-21
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary