5N6U

Crystal structure of Beta-D-Mannosidase from Dictyoglomus thermophilum.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Is the acid/base catalytic residue mutation in beta-d-mannosidase DtMan from Dictyoglomus thermophilum sufficient enough to provide thioglycoligase activity?

Guillotin, L.Richet, N.Lafite, P.Daniellou, R.

(2017) Biochimie 137: 190-196

  • DOI: 10.1016/j.biochi.2017.03.020

  • PubMed Abstract: 
  • Glycoside hydrolases can be turned into thioglycoligase by mutation of the acid/base catalytic carboxylate residue. These mutants have proven valuable to generate S-glycosides, however, few examples in literature have described efficient thioglycolig ...

    Glycoside hydrolases can be turned into thioglycoligase by mutation of the acid/base catalytic carboxylate residue. These mutants have proven valuable to generate S-glycosides, however, few examples in literature have described efficient thioglycoligase activity, and even fewer the underlying molecular mechanism. DtMan, a GH2 family β-d-mannosidase from the thermophilic Dictyoglomus thermophilum was cloned and expressed in E. coli. The recombinant protein is highly specific for β-d-mannosides, and exhibits efficient catalysis constants coupled to thermostability. However, seven variants bearing mutated acid/base residue could not be turned into efficient thioligases. Crystal structure of DtMan Glu425Cys mutant and molecular modeling calculations have demonstrated that unlike other GH2 thioligase reported, active site accessibility of thiol acceptor may be impaired by entrance loop rigidity. This structural feature may explain why DtMan mutants do not exhibit thioglycoligase activity.


    Organizational Affiliation

    Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans, BP 6759, 45067, Orléans Cedex 2, France. Electronic address: pierre.lafite@univ-orleans.fr.,Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans, BP 6759, 45067, Orléans Cedex 2, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-mannosidase
A, B, C, D
836Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12)Mutation(s): 1 
EC: 3.2.1.25
Find proteins for B5YAN4 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12))
Go to UniProtKB:  B5YAN4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 139.250α = 90.00
b = 75.560β = 92.52
c = 217.880γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-16 
  • Released Date: 2017-04-12 
  • Deposition Author(s): Richet, N., Lafite, P.

Funding OrganizationLocationGrant Number
GLYCOPEPSFranceAPR-518N

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Type: Database references
  • Version 1.2: 2017-05-17
    Type: Database references
  • Version 1.3: 2019-02-20
    Type: Advisory, Data collection, Derived calculations