1NOW

Human lysosomal beta-hexosaminidase isoform B in complex with (2R,3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (GalNAc-isofagomine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.218 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Crystal structure of Human beta-hexosaminidase B: Understanding the molecular basis of Sandhoff and Tay-Sachs disease

Mark, B.L.Mahuran, D.J.Cherney, M.M.Zhao, D.Knapp, S.James, M.N.G.

(2003) J Mol Biol 327: 1093-1109

  • DOI: https://doi.org/10.1016/s0022-2836(03)00216-x
  • Primary Citation of Related Structures:  
    1NOU, 1NOW, 1NP0

  • PubMed Abstract: 

    In humans, two major beta-hexosaminidase isoenzymes exist: Hex A and Hex B. Hex A is a heterodimer of subunits alpha and beta (60% identity), whereas Hex B is a homodimer of beta-subunits. Interest in human beta-hexosaminidase stems from its association with Tay-Sachs and Sandhoff disease; these are prototypical lysosomal storage disorders resulting from the abnormal accumulation of G(M2)-ganglioside (G(M2)). Hex A degrades G(M2) by removing a terminal N-acetyl-D-galactosamine (beta-GalNAc) residue, and this activity requires the G(M2)-activator, a protein which solubilizes the ganglioside for presentation to Hex A. We present here the crystal structure of human Hex B, alone (2.4A) and in complex with the mechanistic inhibitors GalNAc-isofagomine (2.2A) or NAG-thiazoline (2.5A). From these, and the known X-ray structure of the G(M2)-activator, we have modeled Hex A in complex with the activator and ganglioside. Together, our crystallographic and modeling data demonstrate how alpha and beta-subunits dimerize to form either Hex A or Hex B, how these isoenzymes hydrolyze diverse substrates, and how many documented point mutations cause Sandhoff disease (beta-subunit mutations) and Tay-Sachs disease (alpha-subunit mutations).


  • Organizational Affiliation

    Canadian Institutes of Heath Research Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, T6G 2H7, Edmonton, Alt., Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-hexosaminidase beta chain
A, B
507Homo sapiensMutation(s): 0 
EC: 3.2.1.52
UniProt & NIH Common Fund Data Resources
Find proteins for P07686 (Homo sapiens)
Explore P07686 
Go to UniProtKB:  P07686
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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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.218 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.391α = 90
b = 112.391β = 90
c = 397.309γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IFGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-29
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2012-11-07
    Changes: Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary