3HG3

Human alpha-galactosidase catalytic mechanism 2. Substrate bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Catalytic mechanism of human alpha-galactosidase.

Guce, A.I.Clark, N.E.Salgado, E.N.Ivanen, D.R.Kulminskaya, A.A.Brumer, H.Garman, S.C.

(2010) J Biol Chem 285: 3625-3632

  • DOI: 10.1074/jbc.M109.060145
  • Primary Citation of Related Structures:  
    3HG2, 3HG3, 3HG4, 3HG5

  • PubMed Abstract: 
  • The enzyme alpha-galactosidase (alpha-GAL, also known as alpha-GAL A; E.C. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. Defects in human alpha-GAL lead to the development of Fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues ...

    The enzyme alpha-galactosidase (alpha-GAL, also known as alpha-GAL A; E.C. 3.2.1.22) is responsible for the breakdown of alpha-galactosides in the lysosome. Defects in human alpha-GAL lead to the development of Fabry disease, a lysosomal storage disorder characterized by the buildup of alpha-galactosylated substrates in the tissues. alpha-GAL is an active target of clinical research: there are currently two treatment options for Fabry disease, recombinant enzyme replacement therapy (approved in the United States in 2003) and pharmacological chaperone therapy (currently in clinical trials). Previously, we have reported the structure of human alpha-GAL, which revealed the overall structure of the enzyme and established the locations of hundreds of mutations that lead to the development of Fabry disease. Here, we describe the catalytic mechanism of the enzyme derived from x-ray crystal structures of each of the four stages of the double displacement reaction mechanism. Use of a difluoro-alpha-galactopyranoside allowed trapping of a covalent intermediate. The ensemble of structures reveals distortion of the ligand into a (1)S(3) skew (or twist) boat conformation in the middle of the reaction cycle. The high resolution structures of each step in the catalytic cycle will allow for improved drug design efforts on alpha-GAL and other glycoside hydrolase family 27 enzymes by developing ligands that specifically target different states of the catalytic cycle. Additionally, the structures revealed a second ligand-binding site suitable for targeting by novel pharmacological chaperones.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-galactosidase AA, B404Homo sapiensMutation(s): 1 
Gene Names: GLA
EC: 3.2.1.22 (PDB Primary Data), 3.2.1.47 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06280 (Homo sapiens)
Explore P06280 
Go to UniProtKB:  P06280
PHAROS:  P06280
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, F4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranoseE, G2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G54976AD
GlyCosmos:  G54976AD
GlyGen:  G54976AD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900037
Query on PRD_900037
E, Galpha-melibioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.548α = 90
b = 106.106β = 90
c = 181.721γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-13
    Changes: Database references, Structure summary