1XSJ

Structure of a Family 31 alpha glycosidase

• PDB DOI: https://doi.org/10.2210/pdb1XSJ/pdb

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


• Deposited: 2004-10-19 Released: 2004-10-26 
• Deposition Author(s): Lovering, A.L., Lee, S.S., Kim, Y.W., Withers, S.G., Strynadka, N.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Literature

Mechanistic and Structural Analysis of a Family 31 alpha-Glycosidase and Its Glycosyl-enzyme Intermediate

Lovering, A.L., Lee, S.S., Kim, Y.W., Withers, S.G., Strynadka, N.C.

(2005) J Biol Chem 280: 2105-2115

• PubMed: 15501829 
• DOI: https://doi.org/10.1074/jbc.M410468200
• Primary Citation of Related Structures:  
  1XSI, 1XSJ, 1XSK


• PubMed Abstract: 
  

  We have determined the first structure of a family 31 alpha-glycosidase, that of YicI from Escherichia coli, both free and trapped as a 5-fluoroxylopyranosyl-enzyme intermediate via reaction with 5-fluoro-alpha-D-xylopyranosyl fluoride. Our 2.2-A resolution structure shows an intimately associated hexamer with structural elements from several monomers converging at each of the six active sites. Our kinetic and mass spectrometry analyses verified several of the features observed in our structural data, including a covalent linkage from the carboxylate side chain of the identified nucleophile Asp(416) to C-1 of the sugar ring. Structure-based sequence comparison of YicI with the mammalian alpha-glucosidases lysosomal alpha-glucosidase and sucrase-isomaltase predicts a high level of structural similarity and provides a foundation for understanding the various mutations of these enzymes that elicit human disease.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 535.48 kDa 
• Atom Count: 38,890 
• Modelled Residue Count: 4,638 
• Deposited Residue Count: 4,668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative family 31 glucosidase yicI	A, B, C, D, E, F	778	Escherichia coli	Mutation(s): 0  Gene Names: yicI EC: 3.2.1
UniProt
Find proteins for P31434 (Escherichia coli (strain K12)) Explore P31434  Go to UniProtKB:  P31434

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth E], P [auth E], Q [auth E], R [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.532	α = 90
b = 224.442	β = 101.75
c = 154.117	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Lovering, A.L., Lee, S.S., Kim, Y.W., Withers, S.G., Strynadka, N.C.

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description