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 

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

  • 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), 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
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit alphaA,
F [auth C],
K [auth E],
P [auth G]
52Homo sapiensMutation(s): 0 
EC: 3.2.1.52
UniProt & NIH Common Fund Data Resources
Find proteins for P06865 (Homo sapiens)
Explore P06865 
Go to UniProtKB:  P06865
PHAROS:  P06865
GTEx:  ENSG00000213614 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06865
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit alphaB [auth I],
G [auth J],
L [auth K],
Q [auth L]
440Homo sapiensMutation(s): 1 
EC: 3.2.1.52
UniProt & NIH Common Fund Data Resources
Find proteins for P06865 (Homo sapiens)
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Go to UniProtKB:  P06865
PHAROS:  P06865
GTEx:  ENSG00000213614 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06865
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P06865-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit betaC [auth B],
H [auth D],
M [auth F],
R [auth H]
58Homo sapiensMutation(s): 0 
EC: 3.2.1.52
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Find proteins for P07686 (Homo sapiens)
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PHAROS:  P07686
GTEx:  ENSG00000049860 
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UniProt GroupP07686
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit beta chain BD [auth M],
I [auth O],
N [auth Q],
S
190Homo sapiensMutation(s): 0 
EC: 3.2.1.52
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Find proteins for P07686 (Homo sapiens)
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PHAROS:  P07686
GTEx:  ENSG00000049860 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07686
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P07686-1
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit beta chain AE [auth N],
J [auth P],
O [auth R],
T
237Homo sapiensMutation(s): 0 
EC: 3.2.1.52
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PHAROS:  P07686
GTEx:  ENSG00000049860 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth d],
U,
V,
W,
Y
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
EA [auth e],
X,
AA [auth a],
BA [auth b],
CA [auth c],
EA [auth e],
X,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGT
Query on NGT

Download Ideal Coordinates CCD File 
FA [auth A]
GA [auth B]
HA [auth C]
IA [auth D]
JA [auth E]
FA [auth A],
GA [auth B],
HA [auth C],
IA [auth D],
JA [auth E],
KA [auth F],
LA [auth G],
MA [auth H]
3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NGT BindingDB:  2GK1 Ki: min: 190, max: 2.70e+5 (nM) from 4 assay(s)
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 3.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary