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 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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

  • DOI: 10.1016/s0022-2836(03)00311-5
  • Primary Citation of Related Structures:  
    1O7A

  • 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 hexosaminidase A (alphabeta), where dimerization is required for catalytic activity ...

    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 Human 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-HEXOSAMINIDASE BETA CHAIN
A, B, C, D, E, F
A, B, C, D, E, F
515Homo sapiensMutation(s): 0 
Gene Names: HEXB, HCC7
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07686
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K, L
G, H, I, J, K, L
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
DA [auth E],
IA [auth F],
JA [auth F],
N [auth A],
S [auth B],
DA [auth E],
IA [auth F],
JA [auth F],
N [auth A],
S [auth B],
X [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
GDL
Query on GDL
Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth E],
HA [auth F],
M [auth A],
R [auth B],
BA [auth D],
CA [auth E],
HA [auth F],
M [auth A],
R [auth B],
W [auth C]
2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone
C8 H13 N O6
NELQYZRSPDCGRQ-DBRKOABJSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth C],
EA [auth E],
FA [auth E],
GA [auth E],
KA [auth F],
AA [auth C],
EA [auth E],
FA [auth E],
GA [auth E],
KA [auth F],
LA [auth F],
MA [auth F],
O [auth A],
P [auth A],
Q [auth A],
T [auth B],
U [auth B],
V [auth B],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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 
  • R-Value Observed: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.931α = 90
b = 163.931β = 90
c = 244.717γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-23
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-04-24
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-10-09
    Changes: Data collection, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-11-18
    Changes: Database references, Structure summary