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- PDB-6q4m: Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation -

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Basic information

Entry
Database: PDB / ID: 6q4m
TitleCrystal structure of the O-GlcNAc transferase Asn648Tyr mutation
ComponentsUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / glycosyltransferase / acceptor peptide / mutation / disease
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / histone acetyltransferase complex / mitophagy / positive regulation of lipid biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / negative regulation of cell migration / cell projection / positive regulation of translation / cellular response to glucose stimulus / mitochondrial membrane / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Regulation of necroptotic cell death / chromatin DNA binding / protein processing / UCH proteinases / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / glutamatergic synapse / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Chem-12V / PHOSPHATE ION / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGundogdu, M. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110061 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation
Authors: Gundogdu, M. / van Aalten, D.M.F.
History
DepositionDec 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 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

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8374
Polymers81,0241
Non-polymers8133
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-17 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.316, 150.736, 199.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1206-

HOH

21A-1389-

HOH

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Components

#1: Protein UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit


Mass: 81023.578 Da / Num. of mol.: 1 / Mutation: N648Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli (E. coli) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Chemical ChemComp-12V / (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE


Mass: 623.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O16P2S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 3.19 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.45 M K2HPO4, 8 mM EDTA and 1% xylitol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→45.92 Å / Num. obs: 52373 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.27 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.92 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.472 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.154 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19886 2638 5 %RANDOM
Rwork0.17464 ---
obs0.17589 49733 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.781 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--3.53 Å20 Å2
3----3.37 Å2
Refinement stepCycle: 1 / Resolution: 2.2→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5519 0 49 370 5938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175248
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6447753
X-RAY DIFFRACTIONr_angle_other_deg1.4351.57112222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66122.969293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94115976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4531530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021128
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9715.1232794
X-RAY DIFFRACTIONr_mcbond_other4.9675.1222793
X-RAY DIFFRACTIONr_mcangle_it7.0017.6663489
X-RAY DIFFRACTIONr_mcangle_other7.0017.6683490
X-RAY DIFFRACTIONr_scbond_it6.1875.7272913
X-RAY DIFFRACTIONr_scbond_other6.0185.7192906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8728.3214253
X-RAY DIFFRACTIONr_long_range_B_refined11.23860.8496517
X-RAY DIFFRACTIONr_long_range_B_other11.17760.6316441
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 174 -
Rwork0.282 3644 -
obs--99.97 %

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