7OP7

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

PDB DOI: https://doi.org/10.2210/pdb7OP7/pdb

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

Deposited: 2021-05-29 Released: 2022-02-02
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.244
R-Value Work: 0.189
R-Value Observed: 0.192

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK. gideon.davies@york.ac.uk.

Macromolecule Content

Total Structure Weight: 200.66 kDa
Atom Count: 14,952
Modelled Residue Count: 1,677
Deposited Residue Count: 1,698
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 EC: 3.2.1.25
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8AAK6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VEE (Subject of Investigation/LOI) Query on VEE Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain NA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth B]	M [auth A], NA [auth B]	(1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol C₁₅ H₃₀ N₄ O₄ GOBIPKNKUJPACR-VQJWOFKYSA-N		Interactions Focus chain M [auth A] Focus chain NA [auth B] Interactions & Density Focus chain M [auth A] Focus chain NA [auth B]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B]	N [auth A] O [auth A] OA [auth B] P [auth A] PA [auth B] N [auth A], 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]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth B] SDF format, chain C [auth A] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain MA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B]	AA [auth A] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth A], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], GB [auth B], H [auth A], HA [auth B], HB [auth B], I [auth A], IA [auth B], IB [auth B], J [auth A], JA [auth B], JB [auth B], K [auth A], KA [auth B], KB [auth B], L [auth A], LA [auth B], MA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain MA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain MA [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] EB [auth B] AB [auth B], BB [auth B], CB [auth B], DB [auth B], EB [auth B], FB [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.244
R-Value Work: 0.189
R-Value Observed: 0.192
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.761	α = 90
b = 114.707	β = 112.89
c = 98.639	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

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