Nicotiana benthamiana alpha-galactosidase

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Nicotiana benthamianaalpha-galactosidase A1.1 can functionally complement human alpha-galactosidase A deficiency associated with Fabry disease.

Kytidou, K.Beekwilder, J.Artola, M.van Meel, E.Wilbers, R.H.P.Moolenaar, G.F.Goosen, N.Ferraz, M.J.Katzy, R.Voskamp, P.Florea, B.I.Hokke, C.H.Overkleeft, H.S.Schots, A.Bosch, D.Pannu, N.Aerts, J.M.F.G.

(2018) J Biol Chem 293: 10042-10058

  • DOI: https://doi.org/10.1074/jbc.RA118.001774
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    α-Galactosidases (EC are retaining glycosidases that cleave terminal α-linked galactose residues from glycoconjugate substrates. α-Galactosidases take part in the turnover of cell wall-associated galactomannans in plants and in the lysosomal degradation of glycosphingolipids in animals. Deficiency of human α-galactosidase A (α-Gal A) causes Fabry disease (FD), a heritable, X-linked lysosomal storage disorder, characterized by accumulation of globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3). Current management of FD involves enzyme-replacement therapy (ERT). An activity-based probe (ABP) covalently labeling the catalytic nucleophile of α-Gal A has been previously designed to study α-galactosidases for use in FD therapy. Here, we report that this ABP labels proteins in Nicotiana benthamiana leaf extracts, enabling the identification and biochemical characterization of an N. benthamiana α-galactosidase we name here A1.1 (gene accession ID GJZM-1660). The transiently overexpressed and purified enzyme was a monomer lacking N -glycans and was active toward 4-methylumbelliferyl-α-d-galactopyranoside substrate ( K m = 0.17 mm) over a broad pH range. A1.1 structural analysis by X-ray crystallography revealed marked similarities with human α-Gal A, even including A1.1's ability to hydrolyze Gb3 and lyso-Gb3, which are not endogenous in plants. Of note, A1.1 uptake into FD fibroblasts reduced the elevated lyso-Gb3 levels in these cells, consistent with A1.1 delivery to lysosomes as revealed by confocal microscopy. The ease of production and the features of A1.1, such as stability over a broad pH range, combined with its capacity to degrade glycosphingolipid substrates, warrant further examination of its value as a potential therapeutic agent for ERT-based FD management.

  • Organizational Affiliation

    From the Departments of Medical Biochemistry.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alpha-galactosidaseA [auth B]363Nicotiana benthamianaMutation(s): 0 
Find proteins for A0A384E148 (Nicotiana benthamiana)
Explore A0A384E148 
Go to UniProtKB:  A0A384E148
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A384E148
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.037α = 90
b = 74.037β = 90
c = 133.307γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description