5I3D

Sulfolobus solfataricus beta-glycosidase - E387Y mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase.

Iglesias-Fernandez, J.Hancock, S.M.Lee, S.S.Khan, M.Kirkpatrick, J.Oldham, N.J.McAuley, K.Fordham-Skelton, A.Rovira, C.Davis, B.G.

(2017) Nat. Chem. Biol. 13: 874-881

  • DOI: 10.1038/nchembio.2394

  • PubMed Abstract: 
  • SNi-like mechanisms, which involve front-face leaving group departure and nucleophile approach, have been observed experimentally and computationally in chemical and enzymatic substitution at α-glycosyl electrophiles. Since SNi-like, SN1 and SN2 subs ...

    SNi-like mechanisms, which involve front-face leaving group departure and nucleophile approach, have been observed experimentally and computationally in chemical and enzymatic substitution at α-glycosyl electrophiles. Since SNi-like, SN1 and SN2 substitution pathways can be energetically comparable, engineered switching could be feasible. Here, engineering of Sulfolobus solfataricus β-glycosidase, which originally catalyzed double SN2 substitution, changed its mode to SNi-like. Destruction of the first SN2 nucleophile through E387Y mutation created a β-stereoselective catalyst for glycoside synthesis from activated substrates, despite lacking a nucleophile. The pH profile, kinetic and mutational analyses, mechanism-based inactivators, X-ray structure and subsequent metadynamics simulations together suggest recruitment of substrates by π-sugar interaction and reveal a quantum mechanics-molecular mechanics (QM/MM) free-energy landscape for the substitution reaction that is similar to those of natural, SNi-like glycosyltransferases. This observation of a front-face mechanism in a β-glycosyltransfer enzyme highlights that SNi-like pathways may be engineered in catalysts with suitable environments and suggests that 'β-SNi' mechanisms may be feasible for natural glycosyltransfer enzymes.


    Organizational Affiliation

    Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), Universitat de Barcelona, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D
489Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 1 
Gene Names: lacS
EC: 3.2.1.23
Find proteins for P22498 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P22498
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PE8
Query on PE8

Download SDF File 
Download CCD File 
A
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.680α = 90.00
b = 129.060β = 90.00
c = 191.760γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
xia2data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references, Source and taxonomy
  • Version 1.2: 2017-06-28
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Database references