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 
  • R-Value Observed: 0.182 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1021/ja057904a
  • Primary Citation of Related Structures:  
    2F2H

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative family 31 glucosidase yicI
A, B, C, D, E
A, B, C, D, E, F
773Escherichia coliMutation(s): 0 
Gene Names: yicI
EC: 3.2.1.177
UniProt
Find proteins for P31434 (Escherichia coli (strain K12))
Explore P31434 
Go to UniProtKB:  P31434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31434
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XTG
Query on XTG

Download Ideal Coordinates CCD File 
EA [auth E]
H [auth A]
LA [auth F]
MA [auth F]
N [auth B]
EA [auth E],
H [auth A],
LA [auth F],
MA [auth F],
N [auth B],
S [auth C],
Y [auth D]
4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE
C17 H23 N O11 S
HQYVHBCTLFPWRQ-ZMFOIVQCSA-N
MPO
Query on MPO

Download Ideal Coordinates CCD File 
DA [auth E],
KA [auth F],
M [auth B],
R [auth C],
X [auth D]
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth E]
G [auth A]
HA [auth F]
IA [auth F]
BA [auth E],
CA [auth E],
G [auth A],
HA [auth F],
IA [auth F],
JA [auth F],
L [auth B],
Q [auth C],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
FA [auth E]
GA [auth E]
I [auth A]
J [auth A]
AA [auth D],
FA [auth E],
GA [auth E],
I [auth A],
J [auth A],
K [auth A],
NA [auth F],
O [auth B],
OA [auth F],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
XTG PDBBind:  2F2H Ki: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.317α = 90
b = 175.841β = 90
c = 210.742γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description