1HP5

STREPTOMYCES PLICATUS BETA-N-ACETYLHEXOSAMINIDASE COMPLEXED WITH INTERMEDIATE ANALOUGE NAG-THIAZOLINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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, 1HP4

  • 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: 
    • 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
    • NAG-thiazoline, An N-acetyl-betahexosaminidase inhibitor that implicates acetamido participation
      Knapp, S., Vocadlo, D., Gao, Z., Kirk, B., Lou, J., Withers, S.G.
      (1996) J Am Chem Soc 118: 6804
    • Cloning and high-level expression of a chitinase-encoding gene of Streptomyces plicatus
      Robbins, P.W., Overbye, K., Albright, C., Benfield, B., Pero, J.
      (1992) Gene 111: 69
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-N-ACETYLHEXOSAMINIDASEA512Streptomyces plicatusMutation(s): 0 
Gene Names: hex
EC: 3.2.1.52
Find proteins for O85361 (Streptomyces plicatus)
Explore O85361 
Go to UniProtKB:  O85361
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGT
Query on NGT

Download CCD File 
A
3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NGTKi:  20000   nM  BindingDB
NGTKi :  280   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.621α = 90
b = 133.621β = 90
c = 174.194γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance