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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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history


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:  
    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 ...

    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 alphaA,
F [auth C],
K [auth E],
P [auth G]
52Homo sapiensMutation(s): 0 
Gene Names: HEXA
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  
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UniProt GroupP06865
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit alphaB [auth I],
G [auth J],
L [auth K],
Q [auth L]
440Homo sapiensMutation(s): 1 
Gene Names: HEXA
EC: 3.2.1.52
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PHAROS:  P06865
GTEx:  ENSG00000213614 
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UniProt GroupP06865
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit betaC [auth B],
H [auth D],
M [auth F],
R [auth H]
58Homo sapiensMutation(s): 0 
Gene Names: HEXBHCC7
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
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit beta chain BD [auth M],
I [auth O],
N [auth Q],
S
190Homo sapiensMutation(s): 0 
Gene Names: HEXBHCC7
EC: 3.2.1.52
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GTEx:  ENSG00000049860 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidase subunit beta chain AE [auth N],
J [auth P],
O [auth R],
T
237Homo sapiensMutation(s): 0 
Gene Names: HEXBHCC7
EC: 3.2.1.52
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GTEx:  ENSG00000049860 
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Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
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