Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 536.21 kDa 
• Atom Count: 39,799 
• Modelled Residue Count: 4,638 
• Deposited Residue Count: 4,638 
• Unique protein chains: 1

 2F2H

Structure of the YicI thiosugar Michaelis complex

• PDB DOI:  https://doi.org/10.2210/pdb2F2H/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-16 Released: 2006-02-28 
• Deposition Author(s): Kim, Y.-W., Lovering, A.L., Strynadka, N.C.J., Withers, S.G.

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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 

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

• PubMed: 16478160 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative family 31 glucosidase yicI	A, B, C, D, E, F	773	Escherichia coli	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XTG	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	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	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	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
ID	Source	Binding Affinity
XTG	Binding MOAD:  2F2H	Ki: 2000 (nM) from 1 assay(s)
	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 = 162.317	α = 90
b = 175.841	β = 90
c = 210.742	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-28 
Deposition Author(s): Kim, Y.-W., Lovering, A.L., Strynadka, N.C.J., Withers, S.G.

Revision History  

• 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