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- PDB-6eou: O-GlcNAc transferase TPR domain with the intellectual disability ... -

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Basic information

Entry
Database: PDB / ID: 6eou
TitleO-GlcNAc transferase TPR domain with the intellectual disability associated mutation L254F
ComponentsUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / intellectual disability associated point mutation in O-GlcNAc transferase tetratricopeptide domain
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 domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGundogdu, M. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110061 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2018
Title: The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix.
Authors: Gundogdu, M. / Llabres, S. / Gorelik, A. / Ferenbach, A.T. / Zachariae, U. / van Aalten, D.M.F.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 11, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit


Theoretical massNumber of molelcules
Total (without water)43,5401
Polymers43,5401
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.000, 203.162, 116.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 / OGT


Mass: 43540.250 Da / Num. of mol.: 1 / Mutation: L254F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: Orthorhombic rod and disc shaped
Crystal growTemperature: 295.2 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na-HEPES and 0.1 M MOPS-HCl pH 7,5, 0.04 M diethylene glycol, 0.04 M triethylene glycol, 0.04 M tetraethylene glycol, 0.04 M pentaethylene glycol, 20 % v/v ethylene glycol and 10 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 13, 2016
RadiationMonochromator: 1st diamond beam splitter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.75→46.58 Å / Num. obs: 54404 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Rrim(I) all: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / Num. unique obs: 3067 / CC1/2: 0.76 / Rpim(I) all: 0.45 / Rrim(I) all: 0.73 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLM7.2.1data reduction
Aimless7.0.010data scaling
MOLREP7.0.010phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W3B

1w3b


Resolution: 1.75→101.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.175 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22681 2582 4.8 %RANDOM
Rwork0.19101 ---
obs0.19268 51770 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.37 Å2
Refinement stepCycle: 1 / Resolution: 1.75→101.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 0 280 2972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192770
X-RAY DIFFRACTIONr_bond_other_d0.0020.022522
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9493768
X-RAY DIFFRACTIONr_angle_other_deg1.18635837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93524.255141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65115446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4921518
X-RAY DIFFRACTIONr_chiral_restr0.1380.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023159
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
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_it3.6863.491380
X-RAY DIFFRACTIONr_mcbond_other3.6633.4881379
X-RAY DIFFRACTIONr_mcangle_it4.7875.2161726
X-RAY DIFFRACTIONr_mcangle_other4.7995.2171727
X-RAY DIFFRACTIONr_scbond_it4.9154.0661390
X-RAY DIFFRACTIONr_scbond_other4.9064.0681388
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.455.8782038
X-RAY DIFFRACTIONr_long_range_B_refined10.66142.6283327
X-RAY DIFFRACTIONr_long_range_B_other8.78542.13240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 201 -
Rwork0.258 3810 -
obs--99.73 %

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