5MEH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.103 
  • R-Value Work: 0.091 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Conformational Behaviour of Azasugars Based on Mannuronic Acid.

van Rijssel, E.R.Janssen, A.P.A.Males, A.Davies, G.J.van der Marel, G.A.Overkleeft, H.S.Codee, J.D.C.

(2017) Chembiochem 18: 1297-1304

  • DOI: 10.1002/cbic.201700080

  • PubMed Abstract: 
  • A set of mannuronic-acid-based iminosugars, consisting of the C-5-carboxylic acid, methyl ester and amide analogues of 1deoxymannorjirimicin (DMJ), was synthesised and their pH-dependent conformational behaviour was studied. Under acidic conditions t ...

    A set of mannuronic-acid-based iminosugars, consisting of the C-5-carboxylic acid, methyl ester and amide analogues of 1deoxymannorjirimicin (DMJ), was synthesised and their pH-dependent conformational behaviour was studied. Under acidic conditions the methyl ester and the carboxylic acid adopted an "inverted" 1 C4 chair conformation as opposed to the "normal" 4 C1 chair at basic pH. This conformational change is explained in terms of the stereoelectronic effects of the ring substituents and it parallels the behaviour of the mannuronic acid ester oxocarbenium ion. Because of this solution-phase behaviour, the mannuronic acid ester azasugar was examined as an inhibitor for a Caulobacter GH47 mannosidase that hydrolyses its substrates by way of a reaction itinerary that proceeds through a 3 H4 transition state. No binding was observed for the mannuronic acid ester azasugar, but sub-atomic resolution data were obtained for the DMJâ‹…CkGH47 complex, showing two conformations-3 S1 and 1 C4 -for the DMJ inhibitor.


    Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.




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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DMJ
Query on DMJ

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Download CCD File 
A
1-DEOXYMANNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-KVTDHHQDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.103 
  • R-Value Work: 0.091 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 145.371α = 90.00
b = 145.371β = 90.00
c = 50.838γ = 120.00
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling
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: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-03-15
    Type: Database references
  • Version 1.2: 2017-04-26
    Type: Database references
  • Version 1.3: 2017-07-12
    Type: Database references
  • Version 1.4: 2017-08-30
    Type: Author supporting evidence