2VO5

Structural and biochemical evidence for a boat-like transition state in beta-mannosidases

• PDB DOI:  https://doi.org/10.2210/pdb2VO5/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-02-08 Released: 2008-04-01 
• Deposition Author(s): Tailford, L.E., Offen, W.A., Smith, N.L., Dumon, C., Moreland, C., Gratien, J., Heck, M.P., Stick, R.V., Bleriot, Y., Vasella, A., Gilbert, H.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.247 
• R-Value Work: 0.169 
• R-Value Observed: 0.173 

Literature

Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases.

Tailford, L.E., Offen, W.A., Smith, N.L., Dumon, C., Morland, C., Gratien, J., Heck, M.P., Stick, R.V., Bleriot, Y., Vasella, A., Gilbert, H.J., Davies, G.J.

(2008) Nat Chem Biol 4: 306

• PubMed: 18408714 
• DOI: https://doi.org/10.1038/nchembio.81
• Primary Citation of Related Structures:  
  2VJX, 2VL4, 2VMF, 2VO5, 2VOT, 2VQT, 2VQU, 2VR4


• PubMed Abstract: 
  

Enzyme inhibition through mimicry of the transition state is a major area for the design of new therapeutic agents. Emerging evidence suggests that many retaining glycosidases that are active on alpha- or beta-mannosides harness unusual B2,5 (boat) transition states. Here we present the analysis of 25 putative beta-mannosidase inhibitors, whose Ki values range from nanomolar to millimolar, on the Bacteroides thetaiotaomicron beta-mannosidase BtMan2A. B2,5 or closely related conformations were observed for all tightly binding compounds. Subsequent linear free energy relationships that correlate log Ki with log Km/kcat for a series of active center variants highlight aryl-substituted mannoimidazoles as powerful transition state mimics in which the binding energy of the aryl group enhances both binding and the degree of transition state mimicry. Support for a B2,5 transition state during enzymatic beta-mannosidase hydrolysis should also facilitate the design and exploitation of transition state mimics for the inhibition of retaining alpha-mannosidases--an area that is emerging for anticancer therapeutics.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 199.52 kDa 
• Atom Count: 14,826 
• Modelled Residue Count: 1,674 
• Deposited Residue Count: 1,692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-MANNOSIDASE	A, B	846	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VBZ	C [auth A], Y [auth B]	(1R,4R,5R,7R,8R)-2-Benzyl-5-hydroxymethyl-2-aza-bicyclo[2.2.2]octane-4,7,8-triol C15 H21 N O4 XOLGFLJPIWWVBX-KJWHEZOQSA-N
BR	L [auth A], M [auth A], OA [auth B], PA [auth B], T [auth A], V [auth A], X [auth A], XA [auth B], YA [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO	AA [auth B], BA [auth B], 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], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], LA [auth B], MA [auth B], NA [auth B], P [auth A], Q [auth A], R [auth A], S [auth A], TA [auth B], U [auth A], UA [auth B], VA [auth B], W [auth A], WA [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	N [auth A], O [auth A], QA [auth B], RA [auth B], SA [auth B], ZA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
VBZ	Binding MOAD:  2VO5	Ki: 1.30e+4 (nM) from 1 assay(s)
	BindingDB:  2VO5	Ki: 1.30e+4 (nM) from 1 assay(s)
	PDBBind:  2VO5	Ki: 1.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.247 
• R-Value Work: 0.169 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.118	α = 90
b = 115.692	β = 113.17
c = 99.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Tailford, L.E., Offen, W.A., Smith, N.L., Dumon, C., Moreland, C., Gratien, J., Heck, M.P., Stick, R.V., Bleriot, Y., Vasella, A., Gilbert, H.J., Davies, G.J.

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance