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- PDB-5uhk: Crystal structure of the core catalytic domain of Human O-GlcNAcase -

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Basic information

Entry
Database: PDB / ID: 5uhk
TitleCrystal structure of the core catalytic domain of Human O-GlcNAcase
Components
  • O-GlcNAcase TIM-barrel domain
  • O-GlcNAcase stalk domain
KeywordsHYDROLASE / O-GLCNACASE / GH84 / ENZYME
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.97 Å
AuthorsKlein, D.J. / Elsen, N.L.
CitationJournal: To Be Published
Title: Crystal structure of the core catalytic domain of human O-GlcNAcase and molecular basis of activity and inhibition
Authors: Elsen, N.L. / Patel, S.B. / Ford, R.E. / Hall, D.L. / Hess, F. / Kandula, H. / Kornienko, M. / Lumb, K.J. / Reid, J. / Selnick, H. / Shipman, J.M. / Sharma, S. / Soisson, S.M. / Klein, D.J.
History
DepositionJan 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: O-GlcNAcase TIM-barrel domain
B: O-GlcNAcase stalk domain
C: O-GlcNAcase TIM-barrel domain
D: O-GlcNAcase stalk domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,8247
Polymers117,5484
Non-polymers2763
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-79 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.800, 96.800, 256.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein O-GlcNAcase TIM-barrel domain / 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: 39987.340 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: Spodoptera frugiperda (fall armyworm)
References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Protein O-GlcNAcase stalk domain / 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: 18786.576 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: Spodoptera frugiperda (fall armyworm)
References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14-17% PEG 3350, 0.2 M Mg Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.97→128 Å / Num. obs: 24942 / % possible obs: 95.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 104.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.3
Reflection shellResolution: 2.97→2.98 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.055 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.927 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.97→34.24 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.878 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.395
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1264 5.09 %RANDOM
Rwork0.194 ---
obs0.197 24840 95.2 %-
Displacement parametersBiso mean: 102.94 Å2
Baniso -1Baniso -2Baniso -3
1--14.9944 Å20 Å20 Å2
2---14.9944 Å20 Å2
3---29.9888 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.97→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 18 6 6936
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017107HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.129609HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2453SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC8
X-RAY DIFFRACTIONt_gen_planes1008HARMONIC8
X-RAY DIFFRACTIONt_it7107HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.98
X-RAY DIFFRACTIONt_other_torsion21.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion875SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8279SEMIHARMONIC4
LS refinement shellResolution: 2.97→3.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.32 167 5.55 %
Rwork0.237 2844 -
all0.241 3011 -
obs--96.32 %

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