3BMX

Beta-N-hexosaminidase (YbbD) from Bacillus subtilis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism

Litzinger, S., Fischer, S., Polzer, P., Diederichs, K., Welte, W., Mayer, C.

(2010) J Biol Chem 285: 35675-35684

  • DOI: 10.1074/jbc.M110.131037
  • Primary Citation of Related Structures:  
    3BMX, 3NVD

  • PubMed Abstract: 

    • Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active si ...

    Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-Å resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-β-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and β-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within β-N-acetylglucosaminidases but otherwise absent in β-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 β-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of β-lactamase.

    Organizational Affiliation: 

    Department of Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized lipoprotein ybbD A, B642Bacillus subtilisMutation(s): 0 
Gene Names: ybbD
EC: 3.2.1.52
Find proteins for P40406 (Bacillus subtilis (strain 168))
Explore P40406 
Go to UniProtKB:  P40406
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.385α = 79.79
b = 73.085β = 69.61
c = 83.567γ = 88.25
Software Package:
Software NamePurpose
PHENIXrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUCCANEERphasing
ARP/wARPmodel building
RESOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2007-12-13 
  • Released Date: 2008-12-16 
    • Deposition Author(s): Fischer, S.

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-29
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Advisory, Refinement description