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- PDB-8p0l: Crystal structure of human O-GlcNAcase in complex with an S-linke... -

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Basic information

Entry
Database: PDB / ID: 8p0l
TitleCrystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide
ComponentsProtein O-GlcNAcase
KeywordsHYDROLASE / Carbohydrate / S-GlcNAc / GH84
Function / homology
Function and homology information


glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding ...glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Acyl-CoA N-acyltransferase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
CYSTEINE / SERINE / Protein O-GlcNAcase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMales, A. / Davies, G.J. / Calvelo, M. / Alteen, M.G. / Vocadlo, D.J. / Rovira, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004819/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2023
Title: Human O -GlcNAcase Uses a Preactivated Boat-skew Substrate Conformation for Catalysis. Evidence from X-ray Crystallography and QM/MM Metadynamics.
Authors: Calvelo, M. / Males, A. / Alteen, M.G. / Willems, L.I. / Vocadlo, D.J. / Davies, G.J. / Rovira, C.
History
DepositionMay 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-GlcNAcase
B: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,4895
Polymers206,0422
Non-polymers4473
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-49 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.499, 101.499, 284.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein O-GlcNAcase / OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma- ...OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma-expressed antigen 5 / N-acetyl-beta-D-glucosaminidase / N-acetyl-beta-glucosaminidase / Nuclear cytoplasmic O-GlcNAcase and acetyltransferase / NCOAT


Mass: 103020.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5 / Production host: Escherichia coli (E. coli)
References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.5→284.62 Å / Num. obs: 52629 / % possible obs: 100 % / Redundancy: 15.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.037 / Rrim(I) all: 0.108 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
10.31-284.6213.30.0325262910.0120.035
2.5-2.5816.50.8444890.8430.30.892

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→95.785 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.049 / SU ML: 0.246 / Cross valid method: FREE R-VALUE / ESU R: 0.301 / ESU R Free: 0.254
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2711 1571 2.991 %
Rwork0.2158 50954 -
all0.218 --
obs-52525 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.096 Å2
Baniso -1Baniso -2Baniso -3
1--4.059 Å2-0 Å20 Å2
2---4.059 Å20 Å2
3---8.117 Å2
Refinement stepCycle: LAST / Resolution: 2.5→95.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 14 26 6995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0117165
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166513
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6449759
X-RAY DIFFRACTIONr_angle_other_deg0.5041.55614920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.39536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.029101051
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.086101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.37810298
X-RAY DIFFRACTIONr_chiral_restr0.0660.21081
X-RAY DIFFRACTIONr_chiral_restr_other0.0440.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021699
X-RAY DIFFRACTIONr_nbd_refined0.2410.21657
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.26483
X-RAY DIFFRACTIONr_nbtor_refined0.1960.23577
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2188
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1170.23
X-RAY DIFFRACTIONr_nbd_other0.2820.215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5660.21
X-RAY DIFFRACTIONr_mcbond_it6.9527.3933582
X-RAY DIFFRACTIONr_mcbond_other6.9487.3933582
X-RAY DIFFRACTIONr_mcangle_it10.17613.2464457
X-RAY DIFFRACTIONr_mcangle_other10.17513.2464458
X-RAY DIFFRACTIONr_scbond_it6.3437.3783583
X-RAY DIFFRACTIONr_scbond_other6.3427.3783584
X-RAY DIFFRACTIONr_scangle_it8.96213.5545301
X-RAY DIFFRACTIONr_scangle_other8.96213.5535302
X-RAY DIFFRACTIONr_lrange_it11.63266.8778250
X-RAY DIFFRACTIONr_lrange_other11.63366.8778251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5650.419940.36937360.37138320.8280.84399.94780.362
2.565-2.6350.3731050.34835940.34836990.8860.8871000.333
2.635-2.7110.3391040.31335180.31436220.9180.9181000.296
2.711-2.7950.403900.30834140.3135040.9010.921000.287
2.795-2.8860.3421150.25933030.26234180.9180.9461000.238
2.886-2.9880.2871060.24432240.24533300.9350.9541000.22
2.988-3.10.37870.23830770.24231640.9080.9571000.212
3.1-3.2270.2821030.22929750.23130780.9420.9621000.209
3.227-3.370.2611080.21928650.22129730.9450.9671000.202
3.37-3.5340.306790.21327540.21528330.9430.9711000.198
3.534-3.7250.257730.21726390.21827120.9560.9731000.206
3.725-3.9510.243770.20424880.20625650.9570.9751000.196
3.951-4.2230.231700.1823860.18124560.9640.981000.174
4.223-4.5610.227820.14821560.1522380.9720.9861000.144
4.561-4.9950.194540.14120480.14221020.9810.9871000.138
4.995-5.5820.197700.15518530.15619230.9810.9861000.152
5.582-6.4420.297440.2116660.21217100.9470.9751000.208
6.442-7.8810.295500.24214240.24414740.9450.9631000.241
7.881-11.1080.254390.18411310.18611700.9580.9791000.191
11.108-95.7850.339210.3447030.3447270.9390.8699.58730.412

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