7ODJ

Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine

PDB DOI: https://doi.org/10.2210/pdb7ODJ/pdb

Classification: HYDROLASE
Organism(s): Cellvibrio mixtus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-04-29 Released: 2022-02-16
Deposition Author(s): McGregor, N.G.S., Davies, G.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.158
R-Value Work: 0.125

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 51 kDa
Atom Count: 3,932
Modelled Residue Count: 409
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Man5A	A [auth AAA]	440	Cellvibrio mixtus	Mutation(s): 0 Gene Names: man5A
UniProt
Find proteins for Q6QT42 (Cellvibrio mixtus) Explore Q6QT42 Go to UniProtKB: Q6QT42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6QT42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 G [auth AAA] MOL2 format, chain G [auth AAA]	G [auth AAA]	(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 G [auth AAA] Interactions & Density Focus chain G [auth AAA]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain B [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain F [auth AAA]	B [auth AAA], C [auth AAA], D [auth AAA], F [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain F [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain F [auth AAA]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] MOL2 format, chain E [auth AAA]	E [auth AAA]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth AAA] Interactions & Density Focus chain E [auth AAA]