2F2H

Structure of the YicI thiosugar Michaelis complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Expanding the Thioglycoligase Strategy to the Synthesis of alpha-linked Thioglycosides Allows Structural Investigation of the Parent Enzyme/Substrate Complex

Kim, Y.-W.Lovering, A.L.Chen, H.Kantner, T.McIntosh, L.P.Strynadka, N.C.J.Withers, S.G.

(2006) J.Am.Chem.Soc. 128: 2202-2203

  • DOI: 10.1021/ja057904a

  • PubMed Abstract: 
  • For the first time, the thioglycoligase strategy has been successfully applied to alpha-glycosidases. The alpha-thioglycoligases derived from the family 31 glycosidases, alpha-xylosidase from E. coli (YicI) and alpha-glucosidase from Sulfolobus solfa ...

    For the first time, the thioglycoligase strategy has been successfully applied to alpha-glycosidases. The alpha-thioglycoligases derived from the family 31 glycosidases, alpha-xylosidase from E. coli (YicI) and alpha-glucosidase from Sulfolobus solfataricus, catalyze thioglycoligase reactions using alpha-glycosyl fluorides and deoxythioglycosides as donors and acceptors, respectively, in yields up to 86%. In addition, we describe the Michaelis complex of YicI using one of the thioglycosides as a nonhydrolyzable substrate analogue and discuss the structural insights this yields into the specificity and mechanism of family 31 alpha-glycosidases and the molecular basis of an associated genetic disease.


    Organizational Affiliation

    Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative family 31 glucosidase yicI
A, B, C, D, E, F
773Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yicI
EC: 3.2.1.177
Find proteins for P31434 (Escherichia coli (strain K12))
Go to UniProtKB:  P31434
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MPO
Query on MPO

Download SDF File 
Download CCD File 
B, C, D, E, F
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
XTG
Query on XTG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE
4-NITROPHENYL-(6-S-ALPHA-D-XYLOPYRANOSYL)-BETA-D-GLUCOPYRANOSIDE
C17 H23 N O11 S
HQYVHBCTLFPWRQ-ZMFOIVQCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XTGKi: 2000 nM BINDINGMOAD
XTGKi: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 162.317α = 90.00
b = 175.841β = 90.00
c = 210.742γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance