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 

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Ligand Structure Quality Assessment 


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
A, B, C, D, E, F
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
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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
G, H, I, J, K
G, H, I, J, K, L
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]
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
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
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
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

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Ligand Structure Quality Assessment 


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