1O7A

Human beta-Hexosaminidase B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The X-Ray Crystal Structure of Human Beta-Hexosaminidase B Provides New Insights Into Sandhoff Disease

Maier, T.Strater, N.Schuette, C.Klingenstein, R.Sandhoff, K.Saenger, W.

(2003) J.Mol.Biol. 328: 669


  • PubMed Abstract: 
  • Human lysosomal beta-hexosaminidases are dimeric enzymes composed of alpha and beta-chains, encoded by the genes HEXA and HEXB. They occur in three isoforms, the homodimeric hexosaminidases B (betabeta) and S (alphaalpha), and the heterodimeric hexos ...

    Human lysosomal beta-hexosaminidases are dimeric enzymes composed of alpha and beta-chains, encoded by the genes HEXA and HEXB. They occur in three isoforms, the homodimeric hexosaminidases B (betabeta) and S (alphaalpha), and the heterodimeric hexosaminidase A (alphabeta), where dimerization is required for catalytic activity. Allelic variations in the HEXA and HEXB genes cause the fatal inborn errors of metabolism Tay-Sachs disease and Sandhoff disease, respectively. Here, we present the crystal structure of a complex of human beta-hexosaminidase B with a transition state analogue inhibitor at 2.3A resolution (pdb 1o7a). On the basis of this structure and previous studies on related enzymes, a retaining double-displacement mechanism for glycosyl hydrolysis by beta-hexosaminidase B is proposed. In the dimer structure, which is derived from an analysis of crystal packing, most of the mutations causing late-onset Sandhoff disease reside near the dimer interface and are proposed to interfere with correct dimer formation. The structure reported here is a valid template also for the dimeric structures of beta-hexosaminidase A and S.


    Related Citations: 
    • Complete Analysis of the Glycosylation and Disulfide Bond Pattern of Human Beta-Hexosaminidase B by Maldi-Ms
      Schuette, C.G.,Weissgerber, J.,Sandhoff, K.
      (2001) Glycobiology 11: 549
    • Synthesis of a Huamn Lysosomal Enzyme, Beta-Hexosaminidase B, Using the Baculaovirus Expression System
      Boose, J.A.,Tifft, C.J.,Proia, R.L.,Myerowitz, R.
      (1990) Protein Expr.Purif. 1: 111


    Organizational Affiliation

    Institut für Chemie Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-HEXOSAMINIDASE BETA CHAIN
A, B, C, D, E, F
515Homo sapiensMutation(s): 0 
Gene 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
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, E, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GDL
Query on GDL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
C8 H13 N O6
NELQYZRSPDCGRQ-DBRKOABJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 163.931α = 90.00
b = 163.931β = 90.00
c = 244.717γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-23
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-04-24
    Type: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-10-09
    Type: Data collection, Derived calculations, Other