Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-1,3-mannobiose and alpha-1,2-mannobiose

Experimental Data Snapshot

  • Resolution: 1.08 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


An Epoxide Intermediate in Glycosidase Catalysis.

Sobala, L.F.Speciale, G.Zhu, S.Raich, L.Sannikova, N.Thompson, A.J.Hakki, Z.Lu, D.Shamsi Kazem Abadi, S.Lewis, A.R.Rojas-Cervellera, V.Bernardo-Seisdedos, G.Zhang, Y.Millet, O.Jimenez-Barbero, J.Bennet, A.J.Sollogoub, M.Rovira, C.Davies, G.J.Williams, S.J.

(2020) ACS Cent Sci 6: 760-770

  • DOI: https://doi.org/10.1021/acscentsci.0c00111
  • Primary Citation of Related Structures:  
    6FWG, 6FWI, 6FWJ, 6FWL, 6FWM, 6FWO, 6FWP, 6FWQ

  • PubMed Abstract: 

    Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo -α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, a sugar-shaped cyclitol β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modeling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unusual flattened, envelope ( E 3 ) conformation. Kinetic isotope effects ( k cat / K M ) for anomeric- 2 H and anomeric- 13 C support an oxocarbenium ion-like transition state, and that for C2- 18 O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.

  • Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyl hydrolase family 71385Bacteroides xylanisolvens XB1AMutation(s): 0 
Gene Names: BXY_34140
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A)
Explore D6D1V7 
Go to UniProtKB:  D6D1V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6D1V7
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G00891MP
GlyCosmos:  G00891MP
GlyGen:  G00891MP
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Biologically Interesting Molecules (External Reference) 2 Unique
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.942α = 90
b = 108.942β = 90
c = 68.525γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322942
Australian Research CouncilAustraliaFT130100103
Australian Research CouncilAustraliaDP120101396
Spanish Ministry of Economy and CompetitivenessSpainCTQ2017-85496-P
Spanish Ministry of Economy and CompetitivenessSpainCTQ2015-64597-C2-1P
Agency for Administration of University and ResearchSpain2017SGR-1189
Generalitat de CatalunyaSpain2014SGR-987

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-08
    Changes: Database references
  • Version 1.3: 2020-07-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-02-03
    Changes: Data collection, Database references, Structure summary