2VJX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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.Moreland, 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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-MANNOSIDASEA, B846Bacteroides thetaiotaomicron VPI-5482Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8AAK6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IFL
Query on IFL

Download Ideal Coordinates CCD File 
C [auth A],
NA [auth B]
(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE
C6 H11 N O4
ARBXEMIAJIJEQI-WDCZJNDASA-N
 Ligand Interaction
BR
Query on BR

Download Ideal Coordinates CCD File 
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GB [auth B],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GB [auth B],
HB [auth B],
KA [auth A]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth B],
BA [auth A],
BB [auth B],
CB [auth B],
AA [auth A],
AB [auth B],
BA [auth A],
BB [auth B],
CB [auth B],
D [auth A],
DB [auth B],
E [auth A],
EB [auth B],
F [auth A],
FB [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
MB [auth B],
N [auth A],
NB [auth B],
O [auth A],
OA [auth B],
OB [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],
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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth A],
HA [auth A],
IA [auth A],
IB [auth B],
JA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
IB [auth B],
JA [auth A],
JB [auth B],
KB [auth B],
LA [auth A],
LB [auth B],
MA [auth A],
PB [auth B],
QB [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IFL PDBBind:  2VJX Ki: 1.10e+4 (nM) from 1 assay(s)
BindingDB:  2VJX Ki: 1.10e+4 (nM) from 1 assay(s)
Binding MOAD:  2VJX Ki: 1.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.366α = 90
b = 114.396β = 113.17
c = 99.677γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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