1HP4

CRYSTAL STRUCTURE OF STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase.

Mark, B.L.Vocadlo, D.J.Knapp, S.Triggs-Raine, B.L.Withers, S.G.James, M.N.

(2001) J.Biol.Chem. 276: 10330-10337

  • DOI: 10.1074/jbc.M011067200
  • Primary Citation of Related Structures:  1HP5

  • PubMed Abstract: 
  • beta-Hexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of beta-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. Heritable deficiency of this enzyme results in various forms of GalNAc-beta(1,4)-[N- ...

    beta-Hexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of beta-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. Heritable deficiency of this enzyme results in various forms of GalNAc-beta(1,4)-[N-acetylneuraminic acid (2,3)]-Gal-beta(1,4)-Glc-ceramide gangliosidosis, including Tay-Sachs disease. We have determined the x-ray crystal structure of a beta-hexosaminidase from Streptomyces plicatus to 2.2 A resolution (Protein Data Bank code ). beta-Hexosaminidases are believed to use a substrate-assisted catalytic mechanism that generates a cyclic oxazolinium ion intermediate. We have solved and refined a complex between the cyclic intermediate analogue N-acetylglucosamine-thiazoline and beta-hexosaminidase from S. plicatus to 2.1 A resolution (Protein Data Bank code ). Difference Fourier analysis revealed the pyranose ring of N-acetylglucosamine-thiazoline bound in the enzyme active site with a conformation close to that of a (4)C(1) chair. A tryptophan-lined hydrophobic pocket envelopes the thiazoline ring, protecting it from solvolysis at the iminium ion carbon. Within this pocket, Tyr(393) and Asp(313) appear important for positioning the 2-acetamido group of the substrate for nucleophilic attack at the anomeric center and for dispersing the positive charge distributed into the oxazolinium ring upon cyclization. This complex provides decisive structural evidence for substrate-assisted catalysis and the formation of a covalent, cyclic intermediate in family 20 beta-hexosaminidases.


    Related Citations: 
    • Cloning and Expression of a Streptomyces plicatus Chitinase (chitinase-63) in Escherichia coli
      Robbins, P.W.,Albright, C.,Benfield, B.
      (1988) J.Biol.Chem. 263: 443
    • Structural and Functional Characterization of Streptomyces plicatus Beta-N-acetylhexosaminidase by Comparative Molecular Modeling and Site-directed Mutagenesis
      Mark, B.L.,Wasney, G.A.,Salo, T.J.,Khan, A.R.,Cao, Z.,Robbins, P.W.,James, M.N.,Triggs-Raine, B.L.
      (1998) J.Biol.Chem. 273: 19618
    • Cloning and High-level Expression of Chitinase-encoding Gene of Streptomyces plicatus
      Robbins, P.W.,Overbye, K.,Albright, C.,Benfield, B.,Pero, J.
      (1992) Gene 111: 69
    • Biochemical and Structural Assessment of the 1-N-Azasugar GalNAc-isofagomine as a Potent Family 20 beta -N-Acetylhexosaminidase Inhibitor.
      Mark, B.L.,Vocadlo, D.J.,Zhao, D.,Knapp, S.,Withers, S.G.,James, M.N.
      (2001) J.Biol.Chem. 276: 42131


    Organizational Affiliation

    Medical Research Council Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-N-ACETYLHEXOSAMINIDASE
A
512Streptomyces plicatusGene Names: hex
Find proteins for O85361 (Streptomyces plicatus)
Go to UniProtKB:  O85361
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 133.100α = 90.00
b = 133.100β = 90.00
c = 176.789γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
SOLVEphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-12-12 
  • Released Date: 2001-04-04 
  • Deposition Author(s): Mark, B.L.

Revision History 

  • Version 1.0: 2001-04-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance