Structure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron in complex with castanospermine

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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Divergence of Catalytic Mechanism within a Glycosidase Family Provides Insight Into Evolution of Carbohydrate Metabolism by Human Gut Flora.

Gloster, T.M.Turkenburg, J.P.Potts, J.R.Henrissat, B.Davies, G.J.

(2008) Chem Biol 15: 1058

  • DOI: https://doi.org/10.1016/j.chembiol.2008.09.005
  • Primary Citation of Related Structures:  
    2JKA, 2JKE, 2JKP

  • PubMed Abstract: 

    Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining alpha-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron alpha-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. 1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining alpha-galactosidase.

  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK. gloster@ysbl.york.ac.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
727Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Find proteins for G8JZS4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore G8JZS4 
Go to UniProtKB:  G8JZS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8JZS4
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
CTS PDBBind:  2JKP Ki: 5.90e+4 (nM) from 1 assay(s)
Binding MOAD:  2JKP Ki: 5.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.566α = 90
b = 111.988β = 100.89
c = 104.134γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description