7OMS

Bs164 in complex with mannocyclophellitol aziridine

PDB DOI: https://doi.org/10.2210/pdb7OMS/pdb

Classification: HYDROLASE
Organism(s): Bacteroides salyersiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-24 Released: 2022-02-02
Deposition Author(s): McGregor, N., Beenakker, T., Kuo, C.L., Wong, C.S., Offren, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B.I., Overkleeft, H., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 ?
R-Value Free: 0.258
R-Value Work: 0.223

Starting Model: experimental
View more details

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: 462.21 kDa
Atom Count: 32,204
Modelled Residue Count: 3,912
Deposited Residue Count: 4,044
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyco_hydro_42M domain-containing protein	A [auth AAA] B [auth DDD] C [auth CCC] D [auth BBB] E [auth FFF] A [auth AAA], B [auth DDD], C [auth CCC], D [auth BBB], E [auth FFF], F [auth EEE]	674	Bacteroides salyersiae	Mutation(s): 0 Gene Names: HMPREF1071_03408
UniProt
Find proteins for I9SUA3 (Bacteroides salyersiae CL02T12C01) Explore I9SUA3 Go to UniProtKB: I9SUA3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I9SUA3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VKH (Subject of Investigation/LOI) Query on VKH Download Ideal Coordinates CCD File SDF format, chain AA [auth FFF] SDF format, chain EA [auth EEE] SDF format, chain I [auth AAA] SDF format, chain N [auth DDD] SDF format, chain T [auth CCC] SDF format, chain X [auth BBB] MOL2 format, chain AA [auth FFF] MOL2 format, chain EA [auth EEE] MOL2 format, chain I [auth AAA] MOL2 format, chain N [auth DDD] MOL2 format, chain T [auth CCC] MOL2 format, chain X [auth BBB] mmCIF format, chain AA [auth FFF] mmCIF format, chain EA [auth EEE] mmCIF format, chain I [auth AAA] mmCIF format, chain N [auth DDD] mmCIF format, chain T [auth CCC] mmCIF format, chain X [auth BBB]	AA [auth FFF] EA [auth EEE] I [auth AAA] N [auth DDD] T [auth CCC] AA [auth FFF], EA [auth EEE], I [auth AAA], N [auth DDD], T [auth CCC], X [auth BBB]	(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		Interactions Focus chain AA [auth FFF] Focus chain EA [auth EEE] Focus chain I [auth AAA] Focus chain N [auth DDD] Focus chain T [auth CCC] Focus chain X [auth BBB] Interactions & Density Focus chain AA [auth FFF] Focus chain EA [auth EEE] Focus chain I [auth AAA] Focus chain N [auth DDD] Focus chain T [auth CCC] Focus chain X [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth EEE] SDF format, chain DA [auth EEE] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain K [auth DDD] SDF format, chain L [auth DDD] SDF format, chain M [auth DDD] SDF format, chain P [auth CCC] SDF format, chain Q [auth CCC] SDF format, chain R [auth CCC] SDF format, chain S [auth CCC] SDF format, chain V [auth BBB] SDF format, chain W [auth BBB] SDF format, chain Z [auth FFF] MOL2 format, chain CA [auth EEE] MOL2 format, chain DA [auth EEE] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain K [auth DDD] MOL2 format, chain L [auth DDD] MOL2 format, chain M [auth DDD] MOL2 format, chain P [auth CCC] MOL2 format, chain Q [auth CCC] MOL2 format, chain R [auth CCC] MOL2 format, chain S [auth CCC] MOL2 format, chain V [auth BBB] MOL2 format, chain W [auth BBB] MOL2 format, chain Z [auth FFF] mmCIF format, chain CA [auth EEE] mmCIF format, chain DA [auth EEE] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain K [auth DDD] mmCIF format, chain L [auth DDD] mmCIF format, chain M [auth DDD] mmCIF format, chain P [auth CCC] mmCIF format, chain Q [auth CCC] mmCIF format, chain R [auth CCC] mmCIF format, chain S [auth CCC] mmCIF format, chain V [auth BBB] mmCIF format, chain W [auth BBB] mmCIF format, chain Z [auth FFF]	CA [auth EEE] DA [auth EEE] G [auth AAA] H [auth AAA] K [auth DDD] CA [auth EEE], DA [auth EEE], G [auth AAA], H [auth AAA], K [auth DDD], L [auth DDD], M [auth DDD], P [auth CCC], Q [auth CCC], R [auth CCC], S [auth CCC], V [auth BBB], W [auth BBB], Z [auth FFF]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth EEE] Focus chain DA [auth EEE] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain K [auth DDD] Focus chain L [auth DDD] Focus chain M [auth DDD] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain R [auth CCC] Focus chain S [auth CCC] Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain Z [auth FFF] Interactions & Density Focus chain CA [auth EEE] Focus chain DA [auth EEE] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain K [auth DDD] Focus chain L [auth DDD] Focus chain M [auth DDD] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain R [auth CCC] Focus chain S [auth CCC] Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain Z [auth FFF]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth FFF] SDF format, chain FA [auth EEE] SDF format, chain J [auth AAA] SDF format, chain O [auth DDD] SDF format, chain U [auth CCC] SDF format, chain Y [auth BBB] MOL2 format, chain BA [auth FFF] MOL2 format, chain FA [auth EEE] MOL2 format, chain J [auth AAA] MOL2 format, chain O [auth DDD] MOL2 format, chain U [auth CCC] MOL2 format, chain Y [auth BBB] mmCIF format, chain BA [auth FFF] mmCIF format, chain FA [auth EEE] mmCIF format, chain J [auth AAA] mmCIF format, chain O [auth DDD] mmCIF format, chain U [auth CCC] mmCIF format, chain Y [auth BBB]	BA [auth FFF] FA [auth EEE] J [auth AAA] O [auth DDD] U [auth CCC] BA [auth FFF], FA [auth EEE], J [auth AAA], O [auth DDD], U [auth CCC], Y [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth FFF] Focus chain FA [auth EEE] Focus chain J [auth AAA] Focus chain O [auth DDD] Focus chain U [auth CCC] Focus chain Y [auth BBB] Interactions & Density Focus chain BA [auth FFF] Focus chain FA [auth EEE] Focus chain J [auth AAA] Focus chain O [auth DDD] Focus chain U [auth CCC] Focus chain Y [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 ?
R-Value Free: 0.258
R-Value Work: 0.223
Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 69.335	α = 92.272
b = 103.959	β = 97.708
c = 170.127	γ = 106.397

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-02-02
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary