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- PDB-1o7a: Human beta-Hexosaminidase B -

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Basic information

Entry
Database: PDB / ID: 1o7a
TitleHuman beta-Hexosaminidase B
ComponentsBETA-HEXOSAMINIDASE BETA CHAIN
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / HEXOSAMINIDASE / LYSOSOMAL / SPHINGOLIPID DEGRADATION / SANDHOFF DISEASE / BA8-BARREL / GLYCOSIDASE
Function / homology
Function and homology information


beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 (Hyaluronan metabolism) / chondroitin sulfate proteoglycan catabolic process / dermatan sulfate proteoglycan catabolic process / Keratan sulfate degradation / CS/DS degradation / Hyaluronan degradation / penetration of zona pellucida / male courtship behavior / N-acetylglucosamine metabolic process ...beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 (Hyaluronan metabolism) / chondroitin sulfate proteoglycan catabolic process / dermatan sulfate proteoglycan catabolic process / Keratan sulfate degradation / CS/DS degradation / Hyaluronan degradation / penetration of zona pellucida / male courtship behavior / N-acetylglucosamine metabolic process / cortical granule / glycosaminoglycan metabolic process / acetylglucosaminyltransferase activity / astrocyte cell migration / beta-N-acetylhexosaminidase activity / N-glycan processing / hyaluronan catabolic process / beta-N-acetylhexosaminidase / phospholipid biosynthetic process / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / azurophil granule / lysosome organization / neuromuscular process controlling balance / oogenesis / single fertilization / myelination / acrosomal vesicle / lysosomal lumen / beta-N-acetylglucosaminidase activity / skeletal system development / locomotory behavior / sensory perception of sound / neuron cellular homeostasis / intracellular calcium ion homeostasis / azurophil granule lumen / regulation of cell shape / carbohydrate binding / lysosome / Neutrophil degranulation / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / identical protein binding / membrane
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
2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone / Beta-hexosaminidase subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.25 Å
AuthorsMaier, T. / Strater, N. / Schuette, C. / Klingenstein, R. / Sandhoff, K. / Saenger, W.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The X-Ray Crystal Structure of Human Beta-Hexosaminidase B Provides New Insights Into Sandhoff Disease
Authors: Maier, T. / Strater, N. / Schuette, C. / Klingenstein, R. / Sandhoff, K. / Saenger, W.
#1: Journal: Glycobiology / Year: 2001
Title: Complete Analysis of the Glycosylation and Disulfide Bond Pattern of Human Beta-Hexosaminidase B by Maldi-Ms
Authors: Schuette, C.G. / Weissgerber, J. / Sandhoff, K.
#2: Journal: Protein Expr.Purif. / Year: 1990
Title: Synthesis of a Human Lysosomal Enzyme, Beta-Hexosaminidase B, Using the Baculaovirus Expression System
Authors: Boose, J.A. / Tifft, C.J. / Proia, R.L. / Myerowitz, R.
History
DepositionOct 29, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Oct 9, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.oper_expression
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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Revision 2.1Nov 18, 2020Group: Database references / Structure summary / Category: chem_comp / citation / Item: _chem_comp.pdbx_synonyms / _citation.title
Revision 2.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
C: BETA-HEXOSAMINIDASE BETA CHAIN
D: BETA-HEXOSAMINIDASE BETA CHAIN
E: BETA-HEXOSAMINIDASE BETA CHAIN
F: BETA-HEXOSAMINIDASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,67439
Polymers353,5546
Non-polymers6,12033
Water41,9032326
1
A: BETA-HEXOSAMINIDASE BETA CHAIN
B: BETA-HEXOSAMINIDASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95314
Polymers117,8512
Non-polymers2,10212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint8 kcal/mol
Surface area37690 Å2
MethodPISA
2
C: BETA-HEXOSAMINIDASE BETA CHAIN
D: BETA-HEXOSAMINIDASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,54610
Polymers117,8512
Non-polymers1,6958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint1 kcal/mol
Surface area37540 Å2
MethodPISA
3
E: BETA-HEXOSAMINIDASE BETA CHAIN
hetero molecules

E: BETA-HEXOSAMINIDASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95314
Polymers117,8512
Non-polymers2,10212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area5230 Å2
ΔGint12 kcal/mol
Surface area39750 Å2
MethodPISA
4
F: BETA-HEXOSAMINIDASE BETA CHAIN
hetero molecules

F: BETA-HEXOSAMINIDASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,39616
Polymers117,8512
Non-polymers2,54414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area5430 Å2
ΔGint15 kcal/mol
Surface area37920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.931, 163.931, 244.717
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
BETA-HEXOSAMINIDASE BETA CHAIN / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE B / N-ACETYL-BETA-GLUCOSAMINIDASE


Mass: 58925.711 Da / Num. of mol.: 6 / Fragment: 42-556
Source method: isolated from a genetically manipulated source
Details: RECOMBINANTLY EXPRESSED FRAGMENT COMPOSED OF RESIDUES 42-556, N-TERMINUS OF MATURE HUMAN ENZYME IS BETWEEN RESIDUE 48 - 50
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACYM-1BETA / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07686, beta-N-acetylhexosaminidase

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Sugars , 3 types, 18 molecules

#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.: 6
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
#3: Sugar
ChemComp-GDL / 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone / 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE


Type: D-saccharide / Mass: 219.192 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H13NO6
#4: 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.: 6
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 , 2 types, 2341 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2326 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsBETA-HEXOSAMINIDASE IS RESPONSIBLE FOR THE DEGRADATION OF GM2 GANGLIOSIDES, AND A VARIETY OF OTHER ...BETA-HEXOSAMINIDASE IS RESPONSIBLE FOR THE DEGRADATION OF GM2 GANGLIOSIDES, AND A VARIETY OF OTHER MOLECULES CONTAINING TERMINAL N-ACETYL HEXOSAMINES, IN THE BRAIN AND OTHER TISSUES.
Has protein modificationY
Sequence detailsEXPRESSED CONSTRUCT CONTAINS RESIDUES 42-TO 556 OF THE PRECURSOR PROTEIN

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP VAPOUR DIFFUSION PROTEIN SOLUTION: 10 MG/ML HEXB IN 10MM SODIUM CITRATE, 100 MM NACL, PH6.0 RESERVOIR SOLUTION: 100 MM SODIUM CITRATE, PH 5.6, 16% (V/V) ETHYLENE GLYCOL, 10%(V/V) ...Details: HANGING DROP VAPOUR DIFFUSION PROTEIN SOLUTION: 10 MG/ML HEXB IN 10MM SODIUM CITRATE, 100 MM NACL, PH6.0 RESERVOIR SOLUTION: 100 MM SODIUM CITRATE, PH 5.6, 16% (V/V) ETHYLENE GLYCOL, 10%(V/V) POLYETHYLENE GLYCOL 8000
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium citrate1reservoirpH5.6
216 %(v/v)ethylene glycol1reservoir
310 %(v/v)PEG80001reservoir
410 mg/mlprotein1drop
510 mMsodium citrate1droppH6.0
6100 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 23, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 180325 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 5.5 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 30 Å / Num. measured all: 1930354 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.25→28.12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4883320.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1708 1 %RANDOM
Rwork0.196 ---
obs0.196 175064 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.6122 Å2 / ksol: 0.340616 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.86 Å26.16 Å20 Å2
2--8.56 Å20 Å2
3----17.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23420 0 402 2326 26148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.25→2.33 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.307 174 1 %
Rwork0.268 17305 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMLIGANDS.TOP
X-RAY DIFFRACTION4LIGANDS.PARION.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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