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- PDB-5m7t: Structure of human O-GlcNAc hydrolase with PugNAc type inhibitor -

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Basic information

Entry
Database: PDB / ID: 5m7t
TitleStructure of human O-GlcNAc hydrolase with PugNAc type inhibitor
ComponentsProtein O-GlcNAcase
KeywordsHYDROLASE / human glacoside hydrolase / GlcNAc
Function / homology
Function and homology information


glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein O-linked glycosylation / protein deglycosylation ...glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein O-linked glycosylation / protein deglycosylation / beta-N-acetylglucosaminidase activity / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Acyl-CoA N-acyltransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-GDV / Protein O-GlcNAcase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRoth, C. / Chan, S. / Offen, W.A. / Hemsworth, G.R. / Willems, L.I. / King, D. / Varghese, V. / Britton, R. / Vocadlo, D.J. / Davies, G.J.
Funding support United Kingdom, Canada, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K003836/1 United Kingdom
Canadian Institutes of Health ResearchMOP-123341 Canada
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structural and functional insight into human O-GlcNAcase.
Authors: Roth, C. / Chan, S. / Offen, W.A. / Hemsworth, G.R. / Willems, L.I. / King, D.T. / Varghese, V. / Britton, R. / Vocadlo, D.J. / Davies, G.J.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)206,7654
Polymers206,0422
Non-polymers7232
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-62 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.146, 101.146, 283.289
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 BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-GDV / (5R,6R,7R,8S)-8-(ACETYLAMINO)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2-CARBOXAMIDE


Mass: 361.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O5

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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: 2.5 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.1-0.2 M tri Ammonium citrate 16-20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→95.44 Å / Num. obs: 46333 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.279 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.59 / Rpim(I) all: 0.634 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→95.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.251
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1411 3.1 %RANDOM
Rwork0.2027 ---
obs0.2037 46237 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 218.95 Å2 / Biso mean: 105.8739 Å2 / Biso min: 50.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2---1.63 Å20 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.6→95.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 0 52 0 7411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197614
X-RAY DIFFRACTIONr_bond_other_d00.027115
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.96310313
X-RAY DIFFRACTIONr_angle_other_deg3.64316386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91623.616365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.638151299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7211549
X-RAY DIFFRACTIONr_chiral_restr0.0960.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218467
X-RAY DIFFRACTIONr_gen_planes_other0.010.021830
X-RAY DIFFRACTIONr_mcbond_it2.4285.5713582
X-RAY DIFFRACTIONr_mcbond_other2.4275.5713581
X-RAY DIFFRACTIONr_mcangle_it3.8318.3484460
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 103 -
Rwork0.355 3232 -
all-3335 -
obs--99.85 %
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)
13.3185-0.8664-0.6113.79170.49912.51040.11880.26880.11970.2974-0.26090.6685-0.0921-0.35810.14210.07310.00290.12450.0689-0.04850.2812-18.9963.14919.385
22.5916-0.504-0.47818.80820.12982.1275-0.0286-0.2451-0.84990.6872-0.114-1.00980.89010.49090.14260.50770.081-0.07430.28960.02360.59859.659-20.11524.866
326.13337.56660.397517.9146.416516.2327-0.30730.6503-1.4057-0.16070.3428-1.11910.24430.7083-0.03540.6809-0.04880.05480.28770.09270.4423-4.953-17.22839.82
44.07490.8446-0.29843.12880.15981.9499-0.0031-0.5759-0.14881.1413-0.0329-0.63620.26130.11940.0360.799-0.0539-0.31140.1277-0.03640.435711.5372.91844.187
53.12952.0897-0.70978.9544-1.76241.9027-0.0059-0.5395-0.49081.30840.07671.14720.454-0.3195-0.07090.8747-0.10330.26690.35070.00680.521-17.925-10.26144.816
611.6421-1.1876-6.88452.81652.53855.3381-1.0339-0.4257-1.42060.8833-0.41940.95551.1215-0.10781.45320.8307-0.03240.22140.61530.09860.9676-11.827-20.8731.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 576
2X-RAY DIFFRACTION2A577 - 678
3X-RAY DIFFRACTION3A679 - 695
4X-RAY DIFFRACTION4B59 - 595
5X-RAY DIFFRACTION5B600 - 663
6X-RAY DIFFRACTION6B664 - 695

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