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- PDB-5uhp: Crystal structure of the core catalytic domain of human O-GlcNAcase -

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Basic information

Entry
Database: PDB / ID: 5uhp
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: 2.79 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 TIM-barrel domain
C: O-GlcNAcase TIM-barrel domain
D: O-GlcNAcase TIM-barrel domain
E: O-GlcNAcase stalk domain
F: O-GlcNAcase stalk domain
G: O-GlcNAcase stalk domain
H: O-GlcNAcase stalk domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,98712
Polymers249,6188
Non-polymers3684
Water66737
1
A: O-GlcNAcase TIM-barrel domain
B: O-GlcNAcase TIM-barrel domain
F: O-GlcNAcase stalk domain
G: O-GlcNAcase stalk domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9936
Polymers124,8094
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-92 kcal/mol
Surface area36540 Å2
MethodPISA
2
C: O-GlcNAcase TIM-barrel domain
D: O-GlcNAcase TIM-barrel domain
E: O-GlcNAcase stalk domain
H: O-GlcNAcase stalk domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9936
Polymers124,8094
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-83 kcal/mol
Surface area36030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.722, 91.531, 94.517
Angle α, β, γ (deg.)77.27, 62.81, 63.03
Int Tables number1
Space group name H-MP1

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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: 43642.105 Da / Num. of mol.: 4
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: 18762.463 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M K Na tartrate tetrahydrate, 20% PEG 3350

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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: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→40.78 Å / Biso Wilson estimate: 73.01 Å2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.79→40.78 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.824 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.227 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.849 / SU Rfree Blow DPI: 0.372 / SU Rfree Cruickshank DPI: 0.392
RfactorNum. reflection% reflectionSelection details
Rfree0.292 3077 5.19 %RANDOM
Rwork0.239 ---
obs0.242 59304 100 %-
Displacement parametersBiso mean: 58.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.937 Å20.0491 Å24.3998 Å2
2--4.9968 Å29.5181 Å2
3----5.9338 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 2.79→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13752 0 24 37 13813
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114123HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1719083HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4882SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes334HARMONIC8
X-RAY DIFFRACTIONt_gen_planes2003HARMONIC8
X-RAY DIFFRACTIONt_it14123HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.96
X-RAY DIFFRACTIONt_other_torsion21.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1739SEMIHARMONIC5
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_contact16269SEMIHARMONIC4
LS refinement shellResolution: 2.79→2.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 220 4.98 %
Rwork0.211 4198 -
all0.213 4418 -
obs--100 %

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