5AGD

An inactive (D125N) variant of the catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with alpha-1,6-mannopentaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Evidence for a Boat Conformation at the Transition State of Gh76 Alpha-1,6-Mannanases- Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism

Thompson, A.J.Speciale, G.Iglesias-Fernandez, J.Hakki, Z.Belz, T.Cartmell, A.Spears, R.J.Chandler, E.Temple, M.J.Stepper, J.Gilbert, H.J.Rovira, C.Williams, S.J.Davies, G.J.

(2015) Angew.Chem.Int.Ed.Engl. 54: 5378

  • DOI: 10.1002/anie.201410502
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • α-Mannosidases and α-mannanases have attracted attention for the insight they provide into nucleophilic substitution at the hindered anomeric center of α-mannosides, and the potential of mannosidase inhibitors as cellular probes and therapeutic agent ...

    α-Mannosidases and α-mannanases have attracted attention for the insight they provide into nucleophilic substitution at the hindered anomeric center of α-mannosides, and the potential of mannosidase inhibitors as cellular probes and therapeutic agents. We report the conformational itinerary of the family GH76 α-mannanases studied through structural analysis of the Michaelis complex and synthesis and evaluation of novel aza/imino sugar inhibitors. A Michaelis complex in an (O) S2 conformation, coupled with distortion of an azasugar in an inhibitor complex to a high energy B2,5 conformation are rationalized through ab initio QM/MM metadynamics that show how the enzyme surface restricts the conformational landscape of the substrate, rendering the B2,5 conformation the most energetically stable on-enzyme. We conclude that GH76 enzymes perform catalysis using an itinerary that passes through (O) S2 and B2,5 (≠) conformations, information that should inspire the development of new antifungal agents.


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-1,6-MANNANASE
A, B
362Bacillus circulansMutation(s): 2 
Gene Names: aman6
Find proteins for Q9Z4P9 (Bacillus circulans)
Go to UniProtKB:  Q9Z4P9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.520α = 90.00
b = 85.725β = 90.00
c = 102.613γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references
  • Version 1.2: 2015-05-06
    Type: Database references
  • Version 1.3: 2017-07-12
    Type: Derived calculations