7OMI

Bs164 in complex with mannocyclophellitol epoxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 

Starting Model: experimental
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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
Glyco_hydro_42M domain-containing protein674Bacteroides salyersiaeMutation(s): 0 
Gene Names: HMPREF1071_03408
UniProt
Find proteins for I9SUA3 (Bacteroides salyersiae CL02T12C01)
Explore I9SUA3 
Go to UniProtKB:  I9SUA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI9SUA3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VKN (Subject of Investigation/LOI)
Query on VKN

Download Ideal Coordinates CCD File 
DA [auth CCC]
GB [auth FFF]
N [auth AAA]
OA [auth DDD]
U [auth BBB]
DA [auth CCC],
GB [auth FFF],
N [auth AAA],
OA [auth DDD],
U [auth BBB],
YA [auth EEE]
(1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
C7 H14 O6
QFYQIWDMMSKNFF-MAFUWASYSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
AA [auth CCC]
CA [auth CCC]
CB [auth FFF]
EB [auth FFF]
K [auth AAA]
AA [auth CCC],
CA [auth CCC],
CB [auth FFF],
EB [auth FFF],
K [auth AAA],
KA [auth DDD],
L [auth AAA],
LA [auth DDD],
Q [auth BBB],
T [auth BBB],
UA [auth EEE],
WA [auth EEE]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth FFF]
BA [auth CCC]
DB [auth FFF]
EA [auth DDD]
FA [auth DDD]
AB [auth FFF],
BA [auth CCC],
DB [auth FFF],
EA [auth DDD],
FA [auth DDD],
FB [auth FFF],
G [auth AAA],
GA [auth DDD],
H [auth AAA],
IA [auth DDD],
J [auth AAA],
JA [auth DDD],
M [auth AAA],
MA [auth DDD],
NA [auth DDD],
O [auth BBB],
PA [auth EEE],
QA [auth EEE],
R [auth BBB],
RA [auth EEE],
S [auth BBB],
TA [auth EEE],
V [auth CCC],
VA [auth EEE],
W [auth CCC],
X [auth CCC],
XA [auth EEE],
Z [auth CCC],
ZA [auth FFF]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth FFF]
HA [auth DDD]
I [auth AAA]
P [auth BBB]
SA [auth EEE]
BB [auth FFF],
HA [auth DDD],
I [auth AAA],
P [auth BBB],
SA [auth EEE],
Y [auth CCC]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.452α = 92.292
b = 104.426β = 97.351
c = 170.781γ = 106.554
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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