6FWM

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-1,2-anhydro-mannose hydrolyzed by enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

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Ligand Structure Quality Assessment 


This is version 1.4 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: 10.1021/acscentsci.0c00111
  • Primary Citation of Related Structures:  
    6FWP, 6FWO, 6FWQ, 6FWG, 6FWJ, 6FWI, 6FWL, 6FWM

  • 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 ...

    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.


    Related Citations: 
    • An Epoxide Intermediate in Glycosidase Catalysis
      Sobala, L.F., Speciale, G., Hakki, Z., Fernandes, P.Z., Raich, L., Rojas-Cervellera, V., Bennet, A., Thompson, A.J., Bernardo-Seisdedos, G., Millet, O., Zhu, S., Lu, D., Sollogoub, M., Rovira, C., Jimenez-Barbero, J., Davies, G.J., Williams, S.J.
      (2019) Chemrxiv --: --

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase family 71A385Bacteroides xylanisolvens XB1AMutation(s): 0 
Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A)
Explore D6D1V7 
Go to UniProtKB:  D6D1V7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
D [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
M96 (Subject of Investigation/LOI)
Query on M96

Download Ideal Coordinates CCD File 
C [auth A](1~{S},2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
C7 H14 O5
TVKYRGWJELUGNG-BIVRFLNRSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.273α = 90
b = 108.273β = 90
c = 67.456γ = 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