1M03 image
Deposition Date 2002-06-11
Release Date 2002-12-11
Last Version Date 2024-10-30
Entry Detail
PDB ID:
1M03
Keywords:
Title:
Mutant Streptomyces plicatus beta-hexosaminidase (D313A) in complex with product (GlcNAc)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.21
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 61 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Beta-N-acetylhexosaminidase
Gene (Uniprot):hex
Mutations:D319A
Chain IDs:A
Chain Length:512
Number of Molecules:1
Biological Source:Streptomyces plicatus
Primary Citation
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.
J.Biol.Chem. 277 40055 40065 (2002)
PMID: 12171933 DOI: 10.1074/jbc.M206481200

Abstact

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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Primary Citation of related structures