1O7A

Human beta-Hexosaminidase B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.236 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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

This is version 2.2 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: https://doi.org/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. 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-HEXOSAMINIDASE BETA CHAIN
A, B, C, D, E
515Homo 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: 2Go to GlyGen: P07686-1
Sequence Annotations
Expand
  • 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
G, H, I, J, K
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / 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]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GDL
Query on GDL

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth E]
HA [auth F]
M [auth A]
R [auth B]
2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone
C8 H13 N O6
NELQYZRSPDCGRQ-DBRKOABJSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth E]
FA [auth E]
GA [auth E]
KA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.236 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
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 

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

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
  • Version 2.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary