6TJQ

Crystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fluoro-beta-D-glucopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

A baculoviral system for the production of human beta-glucocerebrosidase enables atomic resolution analysis.

Rowland, R.J.Wu, L.Liu, F.Davies, G.J.

(2020) Acta Crystallogr D Struct Biol 76: 565-580

  • DOI: https://doi.org/10.1107/S205979832000501X
  • Primary Citation of Related Structures:  
    6TJJ, 6TJK, 6TJQ, 6TN1

  • PubMed Abstract: 

    The lysosomal glycoside hydrolase β-glucocerebrosidase (GBA; sometimes called GBA1 or GC ase ) catalyses the hydrolysis of glycosphingolipids. Inherited deficiencies in GBA cause the lysosomal storage disorder Gaucher disease (GD). Consequently, GBA is of considerable medical interest, with continuous advances in the development of inhibitors, chaperones and activity-based probes. The development of new GBA inhibitors requires a source of active protein; however, the majority of structural and mechanistic studies of GBA today rely on clinical enzyme-replacement therapy (ERT) formulations, which are incredibly costly and are often difficult to obtain in adequate supply. Here, the production of active crystallizable GBA in insect cells using a baculovirus expression system is reported, providing a nonclinical source of recombinant GBA with comparable activity and biophysical properties to ERT preparations. Furthermore, a novel crystal form of GBA is described which diffracts to give a 0.98 Å resolution unliganded structure. A structure in complex with the inactivator 2,4-dinitrophenyl-2-deoxy-2-fluoro-β-D-glucopyranoside was also obtained, demonstrating the ability of this GBA formulation to be used in ligand-binding studies. In light of its purity, stability and activity, the GBA production protocol described here should circumvent the need for ERT formulations for structural and biochemical studies and serve to support GD research.


  • Organizational Affiliation

    Department of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GlucosylceramidaseA [auth BBB]497Homo sapiensMutation(s): 0 
Gene Names: GBAGCGLUC
EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (PDB Primary Data), 3.2.1.104 (PDB Primary Data), 3.2.1.46 (UniProt), 3.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens)
Explore P04062 
Go to UniProtKB:  P04062
PHAROS:  P04062
GTEx:  ENSG00000177628 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04062
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P04062-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth BBB],
Z [auth BBB]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NF8 (Subject of Investigation/LOI)
Query on NF8

Download Ideal Coordinates CCD File 
R [auth BBB](2~{R},3~{S},4~{S},5~{S})-5-fluoranyl-2-(hydroxymethyl)oxane-3,4-diol
C6 H11 F O4
JEWFVWVAXVTBRL-SLPGGIOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth BBB],
D [auth BBB],
F [auth BBB],
J [auth BBB]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth BBB]
H [auth BBB]
I [auth BBB]
K [auth BBB]
L [auth BBB]
G [auth BBB],
H [auth BBB],
I [auth BBB],
K [auth BBB],
L [auth BBB],
M [auth BBB],
N [auth BBB],
O [auth BBB],
P [auth BBB],
Q [auth BBB],
S [auth BBB],
T [auth BBB],
U [auth BBB],
V [auth BBB],
W [auth BBB],
X [auth BBB],
Y [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.112α = 90
b = 76.351β = 101.987
c = 68.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M011151/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary