5NN5

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with 1-deoxynojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of human lysosomal acid alpha-glucosidase-a guide for the treatment of Pompe disease.

Roig-Zamboni, V.Cobucci-Ponzano, B.Iacono, R.Ferrara, M.C.Germany, S.Bourne, Y.Parenti, G.Moracci, M.Sulzenbacher, G.

(2017) Nat Commun 8: 1111-1111

  • DOI: 10.1038/s41467-017-01263-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pompe disease, a rare lysosomal storage disease caused by deficiency of the lysosomal acid α-glucosidase (GAA), is characterized by glycogen accumulation, triggering severe secondary cellular damage and resulting in progressive motor handicap and pre ...

    Pompe disease, a rare lysosomal storage disease caused by deficiency of the lysosomal acid α-glucosidase (GAA), is characterized by glycogen accumulation, triggering severe secondary cellular damage and resulting in progressive motor handicap and premature death. Numerous disease-causing mutations in the gaa gene have been reported, but the structural effects of the pathological variants were unknown. Here we present the high-resolution crystal structures of recombinant human GAA (rhGAA), the standard care of Pompe disease. These structures portray the unbound form of rhGAA and complexes thereof with active site-directed inhibitors, providing insight into substrate recognition and the molecular framework for the rationalization of the deleterious effects of disease-causing mutations. Furthermore, we report the structure of rhGAA in complex with the allosteric pharmacological chaperone N-acetylcysteine, which reveals the stabilizing function of this chaperone at the structural level.


    Organizational Affiliation

    Department of Biology, Federico II University, Complesso Universitario di Monte S. Angelo, Via Cintia 21, 80126, Naples, Italy.,Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Univ, AFMB, 163 Avenue de Luminy, 13288, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Univ, AFMB, 163 Avenue de Luminy, 13288, Marseille, France. Gerlind.Sulzenbacher@afmb.univ-mrs.fr.,Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131, Naples, Italy.,Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, Pozzuoli, 80078, Naples, Italy.,Department of Translational Medical Sciences, Federico II University, Via Pansini 5, 80131, Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysosomal alpha-glucosidase
A
872Homo sapiensMutation(s): 0 
Gene Names: GAA
EC: 3.2.1.20
Find proteins for P10253 (Homo sapiens)
Go to Gene View: GAA
Go to UniProtKB:  P10253
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NOJ
Query on NOJ

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Download CCD File 
A
1-DEOXYNOJIRIMYCIN
MORANOLINE
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 97.486α = 90.00
b = 102.972β = 90.00
c = 129.028γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
REFMACphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references