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- PDB-1now: Human lysosomal beta-hexosaminidase isoform B in complex with (2R... -

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Basic information

Entry
Database: PDB / ID: 1now
TitleHuman lysosomal beta-hexosaminidase isoform B in complex with (2R,3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (GalNAc-isofagomine)
Componentsbeta-hexosaminidase beta chain
KeywordsHYDROLASE / (Beta/alpha)8-barrel / homodimer / family 20 glycosidase
Function / homology
Function and homology information


beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / keratan sulfate catabolic process / Glycosphingolipid metabolism / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / protein metabolic process => GO:0019538 / penetration of zona pellucida / CS/DS degradation ...beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / keratan sulfate catabolic process / Glycosphingolipid metabolism / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / protein metabolic process => GO:0019538 / penetration of zona pellucida / CS/DS degradation / Hyaluronan uptake and degradation / male courtship behavior / glycosaminoglycan metabolic process / cortical granule / neutrophil degranulation / glycosphingolipid metabolic process / acetylglucosaminyltransferase activity / astrocyte cell migration / hyaluronan catabolic process / beta-N-acetylhexosaminidase activity / phospholipid biosynthetic process / maintenance of location in cell / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / lipid storage / ganglioside catabolic process / Glycosphingolipid catabolism / oligosaccharide catabolic process / azurophil granule / oogenesis / lysosome organization / neuromuscular process controlling balance / single fertilization / myelination / lysosomal lumen / acrosomal vesicle / locomotory behavior / skeletal system development / sensory perception of sound / intracellular calcium ion homeostasis / neuron cellular homeostasis / azurophil granule lumen / regulation of cell shape / lysosome / Neutrophil degranulation / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / membrane / identical protein binding
Similarity search - Function
Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IFG / Beta-hexosaminidase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMark, B.L. / Mahuran, D.J. / Cherney, M.M. / Zhao, D. / Knapp, S. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of Human beta-hexosaminidase B: Understanding the molecular basis of Sandhoff and Tay-Sachs disease
Authors: Mark, B.L. / Mahuran, D.J. / Cherney, M.M. / Zhao, D. / Knapp, S. / James, M.N.G.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Nov 7, 2012Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-hexosaminidase beta chain
B: beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,99910
Polymers116,3702
Non-polymers1,6308
Water5,783321
1
A: beta-hexosaminidase beta chain
hetero molecules

A: beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,99510
Polymers116,3702
Non-polymers1,6268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6000 Å2
ΔGint-13 kcal/mol
Surface area37300 Å2
MethodPISA
2
B: beta-hexosaminidase beta chain
hetero molecules

B: beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,00310
Polymers116,3702
Non-polymers1,6348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5230 Å2
ΔGint3 kcal/mol
Surface area37060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.391, 112.391, 397.309
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein beta-hexosaminidase beta chain / N-ACETYL-BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE B


Mass: 58184.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: placenta
References: UniProt: p07686, UniProt: P07686*PLUS, beta-N-acetylhexosaminidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 327 molecules

#3: Chemical ChemComp-IFG / (2R,3R,4S,5R)-2-ACETAMIDO-3,4-DIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE


Mass: 204.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16N2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5 mg/ml HexB [final], 50% saturated ammonium sulfate, and 50 mM potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2001 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent cylindrical Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 74245 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→34.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.49 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.166 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21763 3763 5.1 %RANDOM
Rwork0.19315 ---
obs0.19438 70474 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.941 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20.83 Å20 Å2
2--1.65 Å20 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7756 0 107 321 8184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218095
X-RAY DIFFRACTIONr_bond_other_d0.0030.027165
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.94211003
X-RAY DIFFRACTIONr_angle_other_deg1.1892.98416679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3933954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.204151389
X-RAY DIFFRACTIONr_chiral_restr0.2040.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028850
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021702
X-RAY DIFFRACTIONr_nbd_refined0.1870.31507
X-RAY DIFFRACTIONr_nbd_other0.1360.36807
X-RAY DIFFRACTIONr_nbtor_other0.4180.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.5990
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0620.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1420.384
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.521
X-RAY DIFFRACTIONr_mcbond_it0.551.54798
X-RAY DIFFRACTIONr_mcangle_it1.07627788
X-RAY DIFFRACTIONr_scbond_it1.66533297
X-RAY DIFFRACTIONr_scangle_it2.6664.53215
LS refinement shellResolution: 2.2→2.255 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 296
Rwork0.209 5126
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3344-0.05430.05570.4758-0.11961.23550.0039-0.00570.02460.0570.08120.04520.0018-0.1414-0.08510.02450.03990.00030.08660.03990.072414.082329.442123.403
20.40020.0121-0.25340.4436-0.18860.97040.01890.04780.08310.10770.02580.029-0.1258-0.0105-0.04470.0595-0.03450.01960.03270.00920.101648.98852.282131.8208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA55 - 5526 - 503
2X-RAY DIFFRACTION2BB55 - 5526 - 503

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