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Basic information

Entry
Database: PDB / ID: 5oar
TitleCrystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae
Components(Beta-hexosaminidase) x 2
KeywordsHYDROLASE / Glycosylation / Propeptide / Carbohydrate Biotechnology
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process
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 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Chem-NGT / HEXATANTALUM DODECABROMIDE / Beta-hexosaminidase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSkerlova, J. / Rezacova, P. / Brynda, J. / Pachl, P. / Otwinowski, Z. / Vanek, O.
Funding support Czech Republic, 9items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republicprogram NPU I, project LO1304 Czech Republic
Ministry of Education, Youth and Sports of the Czech Republicprojects LG14009 and LM2015043 CIISB for CMS BIOCEV Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLTC17065 Czech Republic
Czech Academy of SciencesRVO 68378050 Czech Republic
Czech Academy of SciencesRVO 61388963 Czech Republic
BIOCEVERDF CZ.1.05/1.1.00/02.0109 and CZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
Charles University in PragueUNCE 204025/2012 Czech Republic
Charles University in PragueSVV 260079/2014 Czech Republic
Grant Agency of the Czech RepublicGA15-05677S Czech Republic
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide.
Authors: Skerlova, J. / Blaha, J. / Pachl, P. / Hofbauerova, K. / Kukacka, Z. / Man, P. / Pompach, P. / Novak, P. / Otwinowski, Z. / Brynda, J. / Vanek, O. / Rezacova, P.
History
DepositionJun 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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 / pdbx_struct_mod_residue / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _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
B: Beta-hexosaminidase
C: Beta-hexosaminidase
D: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,21229
Polymers130,2184
Non-polymers5,99425
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homologs adopt similar dimer assembly, cross-linking, Chemical crosslinking combined with mass spectrometry was used to corroborate the crystal structure, gel filtration, Size- ...Evidence: homology, Homologs adopt similar dimer assembly, cross-linking, Chemical crosslinking combined with mass spectrometry was used to corroborate the crystal structure, gel filtration, Size-exclusion chromatography confirmed the dimeric assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27990 Å2
ΔGint-157 kcal/mol
Surface area39340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.752, 105.752, 285.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Beta-hexosaminidase


Mass: 8149.980 Da / Num. of mol.: 2 / Fragment: Propeptide UNP residues 19-96 / Source method: isolated from a natural source
Details: glycosylated, proteolytically activated enzyme isolated from natural source; consists of a dimer of two catalytic cores and two associated propeptides. Chain A is a propeptide released ...Details: glycosylated, proteolytically activated enzyme isolated from natural source; consists of a dimer of two catalytic cores and two associated propeptides. Chain A is a propeptide released during proteolytic activation and remains associated with chain B. Chains A and B form a monomer.
Source: (natural) Aspergillus oryzae (mold) / References: UniProt: Q8J2T0, beta-N-acetylhexosaminidase
#2: Protein Beta-hexosaminidase


Mass: 56958.953 Da / Num. of mol.: 2 / Fragment: UNP residues 102-600 / Source method: isolated from a natural source
Details: glycosylated, proteolytically activated enzyme isolated from natural source; consists of a dimer of two catalytic cores and two associated propeptides. Chain A is a propeptide released ...Details: glycosylated, proteolytically activated enzyme isolated from natural source; consists of a dimer of two catalytic cores and two associated propeptides. Chain A is a propeptide released during proteolytic activation and remains associated with chain B. Chains A and B form a monomer.
Source: (natural) Aspergillus oryzae (mold) / References: UniProt: Q8J2T0, beta-N-acetylhexosaminidase

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Sugars , 4 types, 11 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.: 2 / 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.: 1 / 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-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / 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 , 4 types, 191 molecules

#7: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H13NO4S
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: Cl
#9: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br12Ta6
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M ammonium sulfate, 20% PEG 3350 and 100 mM HEPES pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.25 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.3→23.37 Å / Num. obs: 59259 / % possible obs: 81.3 % / Observed criterion σ(I): -3 / Redundancy: 6.011 % / Biso Wilson estimate: 57.452 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 0.994 / Net I/σ(I): 19.6 / Num. measured all: 356227
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.442.6410.5651.9356710.7850.66149.4
2.44-2.613.5640.3613.8874270.9410.40968.5
2.61-2.815.0070.2067.7284090.9830.22783.1
2.81-3.087.2770.12115.4988980.9950.1394.9
3.08-3.437.5590.07523.8181310.9970.0895.1
3.43-3.956.5010.06529.0370820.9950.07193.5
3.95-4.817.4520.04337.1760730.9980.04693.2
4.81-6.687.4430.04238.3347310.9980.04591.7
6.68-23.377.0360.0439.828370.9980.04386

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→23.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.541 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.429 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 2732 5.1 %RANDOM
Rwork0.1886 ---
obs0.1913 50708 72.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 123.24 Å2 / Biso mean: 55.372 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.3→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9115 0 258 179 9552
Biso mean--77.83 38.58 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199676
X-RAY DIFFRACTIONr_bond_other_d0.0050.028586
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.96213401
X-RAY DIFFRACTIONr_angle_other_deg0.7973.00119687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45351136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46424.7483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.109151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71546
X-RAY DIFFRACTIONr_chiral_restr0.0770.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022278
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 101 -
Rwork0.347 1639 -
all-1740 -
obs--32.95 %
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)
10.43180.2015-0.52110.3062-0.27430.6902-0.09940.3203-0.03650.182-0.0150.18430.1207-0.33890.11440.2954-0.24660.28360.388-0.14150.3683-7.30229.256150.64
20.30240.1241-0.39550.4355-0.06041.00110.15540.07320.1370.1914-0.12490.0708-0.0810.0293-0.03050.1886-0.0180.06630.17430.08950.173620.39552.273157.44
30.41770.2895-0.53211.3176-0.1630.7279-0.26570.0087-0.13740.42040.03750.02250.4786-0.01460.22820.6001-0.0530.24480.0568-0.04770.17869.48713.921167.116
41.0311-0.2024-0.58330.3411-0.29790.90980.18760.30150.0292-0.0493-0.1418-0.0156-0.0751-0.0967-0.04580.08470.06310.00070.30560.13260.15221.90149.536129.818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D105 - 599
2X-RAY DIFFRACTION2B103 - 599
3X-RAY DIFFRACTION3C19 - 89
4X-RAY DIFFRACTION4A19 - 88

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