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- PDB-2gjx: Crystallographic structure of human beta-Hexosaminidase A -

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Basic information

Entry
Database: PDB / ID: 2gjx
TitleCrystallographic structure of human beta-Hexosaminidase A
Components(Beta-hexosaminidase ...) x 2
KeywordsHYDROLASE / beta-hexosaminidase A / glycosidase / Tay-Sachs disease / GM2 ganglisode / Tim barrel
Function / homology
Function and homology information


Defective HEXA causes GM2G1 (Hyaluronan metabolism) / 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 / cell morphogenesis involved in neuron differentiation ...Defective HEXA causes GM2G1 (Hyaluronan metabolism) / 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 / cell morphogenesis involved in neuron differentiation / glycosaminoglycan biosynthetic process / male courtship behavior / N-acetylglucosamine metabolic process / cortical granule / glycosaminoglycan metabolic process / neuromuscular process controlling posture / acetylglucosaminyltransferase activity / astrocyte cell migration / beta-N-acetylhexosaminidase activity / sexual reproduction / N-glycan processing / hyaluronan catabolic process / beta-N-acetylhexosaminidase / phospholipid biosynthetic process / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / adult walking behavior / 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 / carbohydrate metabolic process / lysosome / protein heterodimerization activity / intracellular membrane-bounded organelle / Neutrophil degranulation / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / identical protein binding / membrane / cytosol
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
Beta-hexosaminidase subunit alpha / Beta-hexosaminidase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLemieux, M.J. / Mark, B.L. / Cherney, M.M. / Withers, S.G. / Mahuran, D.J. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystallographic structure of human beta-Hexosaminidase A: Interpretation of Tay-Sachs Mutations and Loss of GM2 Ganglioside Hydrolysis
Authors: Lemieux, M.J. / Mark, B.L. / Cherney, M.M. / Withers, S.G. / Mahuran, D.J. / James, M.N.G.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-hexosaminidase alpha chain
B: Beta-hexosaminidase beta chain
C: Beta-hexosaminidase beta chain
D: Beta-hexosaminidase alpha chain
E: Beta-hexosaminidase alpha chain
F: Beta-hexosaminidase beta chain
G: Beta-hexosaminidase beta chain
H: Beta-hexosaminidase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,99227
Polymers466,4068
Non-polymers6,58619
Water2,666148
1
A: Beta-hexosaminidase alpha chain
B: Beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6787
Polymers116,6022
Non-polymers2,0775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-11 kcal/mol
Surface area38820 Å2
MethodPISA
2
C: Beta-hexosaminidase beta chain
D: Beta-hexosaminidase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3547
Polymers116,6022
Non-polymers1,7535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-14 kcal/mol
Surface area38450 Å2
MethodPISA
3
E: Beta-hexosaminidase alpha chain
F: Beta-hexosaminidase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6725
Polymers116,6022
Non-polymers1,0703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint0 kcal/mol
Surface area37900 Å2
MethodPISA
4
G: Beta-hexosaminidase beta chain
H: Beta-hexosaminidase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2888
Polymers116,6022
Non-polymers1,6876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-38 kcal/mol
Surface area38140 Å2
MethodPISA
5
A: Beta-hexosaminidase alpha chain
B: Beta-hexosaminidase beta chain
C: Beta-hexosaminidase beta chain
D: Beta-hexosaminidase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,03314
Polymers233,2034
Non-polymers3,83010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-45 kcal/mol
Surface area71850 Å2
MethodPISA
6
E: Beta-hexosaminidase alpha chain
F: Beta-hexosaminidase beta chain
G: Beta-hexosaminidase beta chain
H: Beta-hexosaminidase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,96013
Polymers233,2034
Non-polymers2,7579
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14910 Å2
ΔGint-55 kcal/mol
Surface area70760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)321.091, 110.536, 129.668
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Beta-hexosaminidase ... , 2 types, 8 molecules ADEHBCFG

#1: Protein
Beta-hexosaminidase alpha chain / N-acetyl- beta-glucosaminidase / Beta-N-acetylhexosaminidase / Hexosaminidase A


Mass: 58416.668 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: human placenta / Source: (natural) Homo sapiens (human) / References: UniProt: P06865, beta-N-acetylhexosaminidase
#2: Protein
Beta-hexosaminidase beta chain


Mass: 58184.879 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: human placenta / Source: (natural) Homo sapiens (human) / References: UniProt: P07686, beta-N-acetylhexosaminidase

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Sugars , 3 types, 15 molecules

#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 7 / Source method: obtained synthetically
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
#5: 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: obtained synthetically / 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, 152 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.47 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 13% pEG 8000, 0.1M NaAcetate, 0.2M thiocyanate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2003
RadiationMonochromator: Double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 111834 / Num. obs: 111512 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.75 / % possible all: 2.08

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Phasing

Phasing MRRfactor: 0.491 / Cor.coef. Fo:Fc: 0.569
Highest resolutionLowest resolution
Rotation3 Å39.87 Å
Translation3 Å39.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.87 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.889 / SU B: 44.596 / SU ML: 0.416 / Cross valid method: THROUGHOUT / ESU R: 1.402 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28822 5525 5 %RANDOM
Rwork0.26867 ---
obs0.26965 105984 99.71 %-
all-111834 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31556 0 428 148 32132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02232966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7951.96444936
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.83253869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.08623.8581576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.372155202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.68615180
X-RAY DIFFRACTIONr_chiral_restr0.0660.24877
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225252
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.316017
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.522930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.51588
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.390
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3420.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 401 -
Rwork0.413 7762 -
obs--99.35 %

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