3THC

Crystal structure of human beta-galactosidase in complex with galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human beta-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases

Ohto, U.Usui, K.Ochi, T.Yuki, K.Satow, Y.Shimizu, T.

(2012) J Biol Chem 287: 1801-1812

  • DOI: 10.1074/jbc.M111.293795
  • Primary Citation of Related Structures:  
    3THC, 3THD

  • PubMed Abstract: 
  • G(M1) gangliosidosis and Morquio B are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. These diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-Gal), which lead to accumulations of the β-Gal substrates, G(M1) ganglioside, and keratan sulfate ...

    G(M1) gangliosidosis and Morquio B are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. These diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-Gal), which lead to accumulations of the β-Gal substrates, G(M1) ganglioside, and keratan sulfate. β-Gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. This study shows the crystal structures of human β-Gal in complex with its catalytic product galactose or with its inhibitor 1-deoxygalactonojirimycin. Human β-Gal is composed of a catalytic TIM barrel domain followed by β-domain 1 and β-domain 2. To gain structural insight into the molecular defects of β-Gal in the above diseases, the disease-causing mutations were mapped onto the three-dimensional structure. Finally, the possible causes of the diseases are discussed.


    Organizational Affiliation

    From the Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-galactosidaseA, B, C, D654Homo sapiensMutation(s): 0 
Gene Names: GLB1ELNR1
EC: 3.2.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for P16278 (Homo sapiens)
Explore P16278 
Go to UniProtKB:  P16278
PHAROS:  P16278
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , IA [auth D] , JA [auth D] , 
AA [auth C],  BA [auth C],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  IA [auth D],  JA [auth D],  KA [auth D],  LA [auth D],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  Y [auth C],  Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GAL (Subject of Investigation/LOI)
Query on GAL

Download Ideal Coordinates CCD File 
DA [auth C], J [auth A], NA [auth D], T [auth B]beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth C], FA [auth C], K [auth A], L [auth A], OA [auth D], PA [auth D], U [auth B], V [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
GA [auth C], HA [auth C], M [auth A], N [auth A], QA [auth D], RA [auth D], W [auth B], X [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth C], I [auth A], MA [auth D], S [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.799α = 90
b = 116.104β = 92.21
c = 140.326γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2011-08-18 
  • Released Date: 2011-12-07 
  • Deposition Author(s): Ohto, U., Shimizu, T.

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary