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- PDB-3gxf: Crystal structure of acid-beta-glucosidase with isofagomine at ne... -

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Basic information

Entry
Database: PDB / ID: 3gxf
TitleCrystal structure of acid-beta-glucosidase with isofagomine at neutral pH
ComponentsGlucosylceramidase
KeywordsHYDROLASE / Alternative initiation / Disease mutation / Disulfide bond / Gaucher disease / Glycoprotein / Glycosidase / Ichthyosis / Lipid metabolism / Lysosome / Membrane / Sphingolipid metabolism
Function / homology
Function and homology information


steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / : / glucosylceramidase / lymphocyte migration ...steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / : / glucosylceramidase / lymphocyte migration / scavenger receptor binding / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / sphingosine biosynthetic process / response to thyroid hormone / autophagosome organization / glucosylceramidase activity / microglial cell proliferation / lysosomal protein catabolic process / glucosyltransferase activity / Glycosphingolipid catabolism / regulation of TOR signaling / microglia differentiation / lipid storage / positive regulation of type 2 mitophagy / ceramide biosynthetic process / brain morphogenesis / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / response to pH / pyramidal neuron differentiation / negative regulation of protein metabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / lysosome organization / response to dexamethasone / neuromuscular process / antigen processing and presentation / hematopoietic stem cell proliferation / response to testosterone / Association of TriC/CCT with target proteins during biosynthesis / motor behavior / negative regulation of interleukin-6 production / establishment of skin barrier / homeostasis of number of cells / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cholesterol metabolic process / mitophagy / negative regulation of MAPK cascade / cell maturation / lysosomal lumen / cellular response to starvation / determination of adult lifespan / respiratory electron transport chain / trans-Golgi network / autophagy / negative regulation of inflammatory response / response to estrogen / cellular response to tumor necrosis factor / T cell differentiation in thymus / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / neuron apoptotic process / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / signaling receptor binding / lysosomal membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / PHOSPHATE ION / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsLieberman, R.L.
CitationJournal: Biochemistry / Year: 2009
Title: Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability.
Authors: Lieberman, R.L. / D'aquino, J.A. / Ringe, D. / Petsko, G.A.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosylceramidase
B: Glucosylceramidase
C: Glucosylceramidase
D: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,27879
Polymers222,5614
Non-polymers7,71875
Water16,304905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20880 Å2
ΔGint-349 kcal/mol
Surface area67580 Å2
MethodPISA
2
A: Glucosylceramidase
B: Glucosylceramidase
hetero molecules

C: Glucosylceramidase
D: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,27879
Polymers222,5614
Non-polymers7,71875
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area19010 Å2
ΔGint-341 kcal/mol
Surface area69450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.311, 92.013, 152.362
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 1 - 497 / Label seq-ID: 1 - 497

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Glucosylceramidase / Beta-glucocerebrosidase / Acid beta-glucosidase / D-glucosyl-N-acylsphingosine glucohydrolase / ...Beta-glucocerebrosidase / Acid beta-glucosidase / D-glucosyl-N-acylsphingosine glucohydrolase / Alglucerase / Imiglucerase


Mass: 55640.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04062, glucosylceramidase
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 976 molecules

#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL


Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M Hepes pH 7.5, SOAK with 500uM isofagomine for 10 min, glycerol in cryo, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→32.12 Å / Num. obs: 103572

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementStarting model: PDB entry '2NSX

2nsx


Resolution: 2.4→32.12 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.825 / SU B: 7.687 / SU ML: 0.178 / SU R Cruickshank DPI: 0.336 / SU Rfree: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5209 5 %RANDOM
Rwork0.178 ---
obs0.182 103572 93.17 %-
all-98363 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.29 Å2 / Biso mean: 27.274 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.17 Å2
2---0.18 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15720 0 426 905 17051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02216573
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9722635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.26551984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89823.444720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.889152516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7051584
X-RAY DIFFRACTIONr_chiral_restr0.1340.22418
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212532
X-RAY DIFFRACTIONr_nbd_refined0.2290.28179
X-RAY DIFFRACTIONr_nbtor_refined0.3130.210812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3350.21107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.216
X-RAY DIFFRACTIONr_mcbond_it0.9781.510183
X-RAY DIFFRACTIONr_mcangle_it1.659216072
X-RAY DIFFRACTIONr_scbond_it2.39837325
X-RAY DIFFRACTIONr_scangle_it3.6844.56563
Refine LS restraints NCS

Dom-ID: 1 / Number: 3930 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.270.5
1AMEDIUM THERMAL0.752
2BMEDIUM POSITIONAL0.250.5
2BMEDIUM THERMAL0.772
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 327 -
Rwork0.238 5942 -
all-6269 -
obs--76.9 %

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