6FWI | pdb_00006fwi

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-mannosamine)

• PDB DOI: https://doi.org/10.2210/pdb6FWI/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides xylanisolvens XB1A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-06 Released: 2019-09-18 
• Deposition Author(s): 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.
• Funding Organization(s): European Research Council, Australian Research Council, Spanish Ministry of Economy and Competitiveness, Agency for Administration of University and Research, Generalitat de Catalunya

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.147 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.124 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

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

• PubMed: 32490192 
• DOI: https://doi.org/10.1021/acscentsci.0c00111
• Primary Citation 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.
School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France.
Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.
Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
Department of Biochemistry and Molecular Biology, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.
Ikerbasque, Basque Foundation for Science, Marıá Dıáz de Haro 3, 48013 Bilbao, Spain.
Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.51 kDa 
• Atom Count: 3,353 
• Modeled Residue Count: 343 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 71	A	385	Bacteroides xylanisolvens XB1A	Mutation(s): 0  Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7  Go to UniProtKB:  D6D1V7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	G [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
E9K	F [auth A]	(1~{R},2~{R},3~{R},4~{R},6~{R})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol C7 H13 N O3 JACJTGDBUDQHPY-NYMZXIIRSA-N
ACT	B [auth A], C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.147 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.124 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.4424526

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.459	α = 90
b = 108.459	β = 90
c = 68.034	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): 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.

---

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	322942
Australian Research Council	Australia	FT130100103
Australian Research Council	Australia	DP120101396
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2017-85496-P
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-64597-C2-1P
Agency for Administration of University and Research	Spain	2017SGR-1189
Generalitat de Catalunya	Spain	2014SGR-987

Revision History  

• 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: Database references, Structure summary
• Version 1.5: 2024-01-17
  Changes: Data collection, Database references, Refinement description