7OP7

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


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 

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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-mannosidase
A, B
849Bacteroides thetaiotaomicron VPI-5482Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8AAK6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VEE (Subject of Investigation/LOI)
Query on VEE

Download Ideal Coordinates CCD File 
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
BR
Query on BR

Download Ideal Coordinates CCD File 
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
CL
Query on CL

Download Ideal Coordinates CCD File 
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
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 = 90.761α = 90
b = 114.707β = 112.89
c = 98.639γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T004819/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R001162/1
European Research Council (ERC)European UnionSynergy Grant 951231-Carbocentre

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, Refinement description