6FWL

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex alpha-Glc-1,3-(1,2-anhydro-carba-mannose)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

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

    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyl hydrolase family 71385Bacteroides xylanisolvens XB1AMutation(s): 1 
Gene Names: BXY_34140
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.233α = 90
b = 108.233β = 90
c = 67.446γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2021-02-03
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2024-01-17
    Changes: Data collection, Database references, Refinement description