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 
  • R-Value Observed: 0.092 

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This is version 1.5 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: https://doi.org/10.1002/cbic.201700080
  • Primary Citation of Related Structures:  
    5MEH

  • 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 the methyl ester and the carboxylic acid adopted an "inverted" 1 C 4 chair conformation as opposed to the "normal" 4 C 1 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 H 4 transition state. No binding was observed for the mannuronic acid ester azasugar, but sub-atomic resolution data were obtained for the DMJ⋅CkGH47 complex, showing two conformations- 3 S 1 and 1 C 4 -for the DMJ inhibitor.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannosyl-oligosaccharide 1,2-alpha-mannosidase447Caulobacter sp. K31Mutation(s): 0 
Gene Names: Caul_4035
EC: 3.2.1.113
UniProt
Find proteins for B0SWV2 (Caulobacter sp. (strain K31))
Explore B0SWV2 
Go to UniProtKB:  B0SWV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0SWV2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMJ
Query on DMJ

Download Ideal Coordinates CCD File 
G [auth A]1-DEOXYMANNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-KVTDHHQDSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.103 
  • R-Value Work: 0.091 
  • R-Value Observed: 0.092 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.371α = 90
b = 145.371β = 90
c = 50.838γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-03-15
    Changes: Database references
  • Version 1.2: 2017-04-26
    Changes: Database references
  • Version 1.3: 2017-07-12
    Changes: Database references
  • Version 1.4: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations