5NE5

Crystal structure of family 47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with kifunensine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach.

Males, A.Raich, L.Williams, S.J.Rovira, C.Davies, G.J.

(2017) Chembiochem 18: 1496-1501

  • DOI: 10.1002/cbic.201700166

  • PubMed Abstract: 
  • The varied yet family-specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly binding and specific enzyme inhibitors. A cardinal example of a GH-family-specific inhibitor, ...

    The varied yet family-specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly binding and specific enzyme inhibitors. A cardinal example of a GH-family-specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is a low-nanomolar inhibitor that is selective for GH family 47 inverting α-mannosidases. Here we show, through quantum-mechanical approaches, that kifunensine is restrained to a "ring-flipped" 1 C4 conformation with another accessible, but higher-energy, region around the 1,4 B conformation. The conformations of kifunensine in complex with a range of GH47 enzymes-including an atomic-level resolution (1 Å) structure of kifunensine with Caulobacter sp. CkGH47 reported herein and with GH family 38 and 92 α-mannosidases-were mapped onto the kifunensine free-energy landscape. These studies revealed that kifunensine has the ability to mimic the product state of GH47 enzymes but cannot mimic any conformational states relevant to the reaction coordinate of mannosidases from other families.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, The University of York, York, YO10 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mannosyl-oligosaccharide 1,2-alpha-mannosidase
A
447Caulobacter sp. (strain K31)Mutation(s): 0 
EC: 3.2.1.113
Find proteins for B0SWV2 (Caulobacter sp. (strain K31))
Go to UniProtKB:  B0SWV2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BTB
Query on BTB

Download SDF File 
Download CCD File 
A
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
KIF
Query on KIF

Download SDF File 
Download CCD File 
A
KIFUNENSINE
C8 H12 N2 O6
OIURYJWYVIAOCW-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.146 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 144.923α = 90.00
b = 144.923β = 90.00
c = 50.593γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
xia2data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence