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 

wwPDB Validation 3D Report Full Report


This is version 2.1 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

  • 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), S ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase subunit alpha
A, C, E, G
52Homo sapiensGene Names: HEXA
EC: 3.2.1.52
Find proteins for P06865 (Homo sapiens)
Go to Gene View: HEXA
Go to UniProtKB:  P06865
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase subunit alpha
I, J, K, L
440Homo sapiensGene Names: HEXA
EC: 3.2.1.52
Find proteins for P06865 (Homo sapiens)
Go to Gene View: HEXA
Go to UniProtKB:  P06865
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase subunit beta
B, D, F, H
58Homo sapiensGene Names: HEXB
EC: 3.2.1.52
Find proteins for P07686 (Homo sapiens)
Go to Gene View: HEXB
Go to UniProtKB:  P07686
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase subunit beta chain B
M, O, Q, S
190Homo sapiensGene Names: HEXB
EC: 3.2.1.52
Find proteins for P07686 (Homo sapiens)
Go to Gene View: HEXB
Go to UniProtKB:  P07686
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase subunit beta chain A
N, P, R, T
237Homo sapiensGene Names: HEXB
EC: 3.2.1.52
Find proteins for P07686 (Homo sapiens)
Go to Gene View: HEXB
Go to UniProtKB:  P07686
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C, G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NGT
Query on NGT

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, 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
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NGTKi: 270000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.274 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 322.246α = 90.00
b = 109.796β = 91.48
c = 132.764γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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