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Basic information

Entry
Database: PDB / ID: 7ezt
TitleThe structure and functional mechanism of nucleotide regulated acetylhexosaminidase Am2136 from Akkermansia muciniphila
Components(Beta-N-acetylhexosaminidaseHexosaminidase) x 4
KeywordsHYDROLASE / Akkermansia Muciniphila Glycosidase Mucin
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / polysaccharide catabolic process
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-hexosaminidase Amuc_2136
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsBao, R. / Li, C.C. / Tang, X.Y. / Zhu, Y.B. / Song, Y.J. / Zhao, N.L. / Huang, Q. / Mou, X.Y. / Luo, G.H. / Liu, T.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81670008 China
CitationJournal: Gut Microbes / Year: 2022
Title: Nucleotide binding as an allosteric regulatory mechanism for Akkermansia muciniphila beta- N -acetylhexosaminidase Am2136.
Authors: Li, C.C. / Yi, H. / Wang, Y.M. / Tang, X.Y. / Zhu, Y.B. / Song, Y.J. / Zhao, N.L. / Huang, Q. / Mou, X.Y. / Luo, G.H. / Liu, T.G. / Yang, G.L. / Zeng, Y.J. / Wang, L.J. / Tang, H. / Fan, G. / Bao, R.
History
DepositionJun 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,0908
Polymers328,9934
Non-polymers974
Water3,639202
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7902
Polymers82,7661
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-6 kcal/mol
Surface area29700 Å2
MethodPISA
2
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7192
Polymers81,6951
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-6 kcal/mol
Surface area29260 Å2
MethodPISA
3
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1052
Polymers82,0811
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area29820 Å2
MethodPISA
4
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4762
Polymers82,4521
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.200, 119.505, 161.931
Angle α, β, γ (deg.)90.000, 103.401, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 82765.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_2136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UPR7, beta-N-acetylhexosaminidase
#2: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 81694.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_2136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UPR7, beta-N-acetylhexosaminidase
#3: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 82081.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_2136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UPR7, beta-N-acetylhexosaminidase
#4: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 82451.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_2136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UPR7, beta-N-acetylhexosaminidase

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Non-polymers , 2 types, 206 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2M Li2SO4, 25% w/v PEG3350, 0.1M HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.81→30 Å / Num. obs: 86269 / % possible obs: 99.2 % / Redundancy: 13.7 % / Biso Wilson estimate: 43.94 Å2 / CC1/2: 0.89 / Rpim(I) all: 0.065 / Net I/σ(I): 11.6
Reflection shellResolution: 2.81→3.02 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 8562 / Rpim(I) all: 0.244

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JQF

6jqf


Resolution: 2.81→26.44 Å / SU ML: 0.3019 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 25.7823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 1999 2.32 %
Rwork0.1937 84132 -
obs0.195 86131 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.07 Å2
Refinement stepCycle: LAST / Resolution: 2.81→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22923 0 4 202 23129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008623565
X-RAY DIFFRACTIONf_angle_d1.352431954
X-RAY DIFFRACTIONf_chiral_restr0.08013440
X-RAY DIFFRACTIONf_plane_restr0.00894147
X-RAY DIFFRACTIONf_dihedral_angle_d8.17983193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.3431400.28675901X-RAY DIFFRACTION97.75
2.88-2.960.3441470.25496027X-RAY DIFFRACTION99.39
2.96-3.040.27681490.23715984X-RAY DIFFRACTION99.34
3.04-3.140.29511280.23876024X-RAY DIFFRACTION99.05
3.14-3.250.2791500.21615899X-RAY DIFFRACTION97.63
3.25-3.380.26081420.19925990X-RAY DIFFRACTION99.58
3.38-3.540.21591440.196055X-RAY DIFFRACTION99.66
3.54-3.720.23741380.17936040X-RAY DIFFRACTION99.61
3.72-3.950.23781460.17466026X-RAY DIFFRACTION99.45
3.96-4.260.23781400.16756036X-RAY DIFFRACTION99.24
4.26-4.690.21871410.15285967X-RAY DIFFRACTION98.33
4.69-5.360.19821450.1616030X-RAY DIFFRACTION98.83
5.36-6.730.23971480.21176090X-RAY DIFFRACTION99.79
6.73-7.80.26491410.20456063X-RAY DIFFRACTION97.55
Refinement TLS params.Method: refined / Origin x: -14.6705518087 Å / Origin y: -18.3248207802 Å / Origin z: -40.076552862 Å
111213212223313233
T0.235088180225 Å2-0.0118556598925 Å20.0132734189554 Å2-0.219372337743 Å20.00831775769557 Å2--0.190997572834 Å2
L0.189475057576 °2-0.0296849562602 °20.0666686223336 °2-0.271618901646 °2-0.0321055044387 °2--0.252974223445 °2
S0.00303226702507 Å °-0.00502497577975 Å °0.0488762236518 Å °0.0514625499893 Å °-0.0119066267253 Å °0.0035051605529 Å °0.00799543097636 Å °-0.0442350610492 Å °0.00663411032686 Å °
Refinement TLS groupSelection details: all

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