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 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.4 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
  • Primary Citation of Related Structures:  
    5N6U

  • 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 thioglycoligase activity, and even fewer the underlying molecular mechanism ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-mannosidaseA, B, C, D836Dictyoglomus thermophilum H-6-12Mutation(s): 1 
Gene Names: DICTH_1692
EC: 3.2.1.25
UniProt
Find proteins for B5YAN4 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12))
Explore B5YAN4 
Go to UniProtKB:  B5YAN4
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.25α = 90
b = 75.56β = 92.52
c = 217.88γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



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  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary