Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 200.48 kDa 
• Atom Count: 14,789 
• Modelled Residue Count: 1,676 
• Deposited Residue Count: 1,698 
• Unique protein chains: 1

 7OP6

Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured cyclophellitol aziridine

• PDB DOI:  https://doi.org/10.2210/pdb7OP6/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-29 Released: 2022-05-18 
• Deposition Author(s): McGregor, N.G.S., Beenakker, T.J.M., Kuo, C., Wong, C., Offen, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B.I., Overkleeft, H.S., Davies, G.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.233 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases.

McGregor, N.G.S., Kuo, C.L., Beenakker, T.J.M., Wong, C.S., Offen, W.A., Armstrong, Z., Florea, B.I., Codee, J.D.C., Overkleeft, H.S., Aerts, J.M.F.G., Davies, G.J.

(2022) Org Biomol Chem 20: 877-886

• PubMed: 35015006 
• DOI: https://doi.org/10.1039/d1ob02287c
• Primary Citation of Related Structures:  
  7ODJ, 7OMI, 7OMS, 7OP6, 7OP7


• PubMed Abstract: 
  

Exo -β-mannosidases are a broad class of stereochemically retaining hydrolases that are essential for the breakdown of complex carbohydrate substrates found in all kingdoms of life. Yet the detection of exo -β-mannosidases in complex biological samples remains challenging, necessitating the development of new methodologies. Cyclophellitol and its analogues selectively label the catalytic nucleophiles of retaining glycoside hydrolases, making them valuable tool compounds. Furthermore, cyclophellitol can be readily redesigned to enable the incorporation of a detection tag, generating activity-based probes (ABPs) that can be used to detect and identify specific glycosidases in complex biological samples. Towards the development of ABPs for exo -β-mannosidases, we present a concise synthesis of β- manno -configured cyclophellitol, cyclophellitol aziridine, and N -alkyl cyclophellitol aziridines. We show that these probes covalently label exo -β-mannosidases from GH families 2, 5, and 164. Structural studies of the resulting complexes support a canonical mechanism-based mode of action in which the active site nucleophile attacks the pseudoanomeric centre to form a stable ester linkage, mimicking the glycosyl enzyme intermediate. Furthermore, we demonstrate activity-based protein profiling using an N -alkyl aziridine derivative by specifically labelling MANBA in mouse kidney tissue. Together, these results show that synthetic manno -configured cyclophellitol analogues hold promise for detecting exo -β-mannosidases in biological and biomedical research.

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Organizational Affiliation: 

York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-mannosidase	A, B	849	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_0458
UniProt
Find proteins for Q8AAK6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AAK6  Go to UniProtKB:  Q8AAK6

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JIW (Subject of Investigation/LOI)	FA [auth A]	beta-D-manno-configured cyclophellitol aziridine, reacted form C7 H15 N O5 SWVTZDDSAFUTKS-DOMFMGKQSA-N
VKH	LB [auth B]	(1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol C7 H16 N O4 FGLYJEXIORSHSO-PAMBMQIZSA-O
JIT (Subject of Investigation/LOI)	GA [auth B]	beta-D-manno-configured cyclophellitol aziridine C7 H13 N O4 GPIFFOGPRPKRHS-IVZITJRKSA-N
BR	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], HA [auth B], IA [auth B], JA [auth B], KA [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO	AB [auth B], BB [auth B], I [auth A], J [auth A], K [auth A], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	AA [auth A], BA [auth A], CA [auth A], CB [auth B], DB [auth B], EB [auth B], FB [auth B], GB [auth B], HB [auth B], IB [auth B], JB [auth B], X [auth A], Y [auth A], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	DA [auth A], EA [auth A], KB [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.233 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.92	α = 90
b = 116.858	β = 114.15
c = 100.844	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): McGregor, N.G.S., Beenakker, T.J.M., Kuo, C., Wong, C., Offen, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B.I., Overkleeft, H.S., Davies, G.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T004819/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R001162/1
European Research Council (ERC)	European Union	Synergy Grant 951231-Carbocentre.

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release