5MEL

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with Glc-alpha-1,3-(3R,4R,5R)-5-(hydroxymethyl)cyclohex-1,2-ene-3,4-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.

Petricevic, M.Sobala, L.F.Fernandes, P.Z.Raich, L.Thompson, A.J.Bernardo-Seisdedos, G.Millet, O.Zhu, S.Sollogoub, M.Jimenez-Barbero, J.Rovira, C.Davies, G.J.Williams, S.J.

(2017) J. Am. Chem. Soc. 139: 1089-1097

  • DOI: 10.1021/jacs.6b10075
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools, and ...

    Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools, and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases, members of glycoside hydrolase family 99 (GH99), are interesting targets for inhibitor development as they play key roles in N-glycan maturation and microbiotal yeast mannan degradation, respectively. These enzymes are proposed to act via a 1,2-anhydrosugar "epoxide" mechanism that proceeds through an unusual conformational itinerary. Here, we explore how shape and charge contribute to binding of diverse inhibitors of these enzymes. We report the synthesis of neutral dideoxy, glucal and cyclohexenyl disaccharide inhibitors, their binding to GH99 endo-α-1,2-mannanases, and their structural analysis by X-ray crystallography. Quantum mechanical calculations of the free energy landscapes reveal how the neutral inhibitors provide shape but not charge mimicry of the proposed intermediate and transition state structures. Building upon the knowledge of shape and charge contributions to inhibition of family GH99 enzymes, we design and synthesize α-Man-1,3-noeuromycin, which is revealed to be the most potent inhibitor (KD 13 nM for Bacteroides xylanisolvens GH99 enzyme) of these enzymes yet reported. This work reveals how shape and charge mimicry of transition state features can enable the rational design of potent inhibitors.


    Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycosyl hydrolase family 71
A
385Bacteroides xylanisolvens XB1AMutation(s): 1 
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A)
Go to UniProtKB:  D6D1V7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
7LQ
Query on 7LQ

Download SDF File 
Download CCD File 
A
(1~{R},2~{R},6~{R})-6-(hydroxymethyl)cyclohex-3-ene-1,2-diol
C7 H12 O3
JIULRVIFQNXLCR-FSDSQADBSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.119 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 108.791α = 90.00
b = 108.791β = 90.00
c = 67.850γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
XDSdata reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322942
Australian Research CouncilAustraliaFT130100103
Australian Research CouncilAustraliaDP120101396
Spanish Ministry of Economy and CompetitivenessSpainCTQ2014-55174
Spanish Ministry of Economy and CompetitivenessSpainCTQ2015-64597-C2-1P
Spanish Ministry of Economy and CompetitivenessSpainCTQ2015-68756-R
Generalitat de CatalunyaSpain2014SGR-987

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-02-08
    Type: Database references