2GK1

X-ray crystal structure of NGT-bound HexA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report



Literature

Crystallographic Structure of Human beta-Hexosaminidase A: Interpretation of Tay-Sachs Mutations and Loss of G(M2) Ganglioside Hydrolysis.

Lemieux, M.J.Mark, B.L.Cherney, M.M.Withers, S.G.Mahuran, D.J.James, M.N.

(2006) J Mol Biol 359: 913-929

  • DOI: 10.1016/j.jmb.2006.04.004
  • Primary Citation of Related Structures:  
    2GK1, 2GJX

  • PubMed Abstract: 
  • Lysosomal beta-hexosaminidase A (Hex A) is essential for the degradation of GM2 gangliosides in the central and peripheral nervous system. Accumulation of GM2 leads to severely debilitating neurodegeneration associated with Tay-Sachs disease (TSD), Sando ...

    Lysosomal beta-hexosaminidase A (Hex A) is essential for the degradation of GM2 gangliosides in the central and peripheral nervous system. Accumulation of GM2 leads to severely debilitating neurodegeneration associated with Tay-Sachs disease (TSD), Sandoff disease (SD) and AB variant. Here, we present the X-ray crystallographic structure of Hex A to 2.8 A resolution and the structure of Hex A in complex with NAG-thiazoline, (NGT) to 3.25 A resolution. NGT, a mechanism-based inhibitor, has been shown to act as a chemical chaperone that, to some extent, prevents misfolding of a Hex A mutant associated with adult onset Tay Sachs disease and, as a result, increases the residual activity of Hex A to a level above the critical threshold for disease. The crystal structure of Hex A reveals an alphabeta heterodimer, with each subunit having a functional active site. Only the alpha-subunit active site can hydrolyze GM2 gangliosides due to a flexible loop structure that is removed post-translationally from beta, and to the presence of alphaAsn423 and alphaArg424. The loop structure is involved in binding the GM2 activator protein, while alphaArg424 is critical for binding the carboxylate group of the N-acetyl-neuraminic acid residue of GM2. The beta-subunit lacks these key residues and has betaAsp452 and betaLeu453 in their place; the beta-subunit therefore cleaves only neutral substrates efficiently. Mutations in the alpha-subunit, associated with TSD, and those in the beta-subunit, associated with SD are discussed. The effect of NGT binding in the active site of a mutant Hex A and its effect on protein function is discussed.


    Organizational Affiliation

    CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit alpha ACEG52Homo sapiensMutation(s): 0 
Gene Names: HEXA
EC: 3.2.1.52
Find proteins for P06865 (Homo sapiens)
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Go to UniProtKB:  P06865
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PHAROS:  P06865
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit alpha IJKL440Homo sapiensMutation(s): 1 
Gene Names: HEXA
EC: 3.2.1.52
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PHAROS:  P06865
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit beta BDFH58Homo sapiensMutation(s): 0 
Gene Names: HEXBHCC7
EC: 3.2.1.52
Find proteins for P07686 (Homo sapiens)
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PHAROS:  P07686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit beta chain B MOQS190Homo sapiensMutation(s): 0 
Gene Names: HEXBHCC7
EC: 3.2.1.52
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit beta chain A NPRT237Homo sapiensMutation(s): 0 
Gene Names: HEXBHCC7
EC: 3.2.1.52
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
U, V, W, Y, d
3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
X, Z, a, b, c, e
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NGTKi:  270000   nM  BindingDB
NGTKi:  290   nM  BindingDB
NGTKi:  270   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.277 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 322.246α = 90
b = 109.796β = 91.48
c = 132.764γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2017-08-16
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2017-10-18
    Changes: Refinement description
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary