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- PDB-5npr: The human O-GlcNAc transferase in complex with a thiol-linked bis... -

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Basic information

Entry
Database: PDB / ID: 5npr
TitleThe human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor
Components
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
  • bisubstrate inhibitor
KeywordsTRANSFERASE / O-GlcNAc transferase / GT-B / Rossman-Fold / active site / inhibitor
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation ...protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / 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 / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / mitophagy / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / negative regulation of cell migration / response to nutrient / cell projection / positive regulation of translation / mitochondrial membrane / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / glutamatergic synapse / apoptotic process / regulation of transcription by RNA polymerase II / 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 1 / Tetratricopeptide repeat / 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 1 / 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-94T / : / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRafie, K. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110061 United Kingdom
CitationJournal: Bioconjug. Chem. / Year: 2018
Title: Thio-Linked UDP-Peptide Conjugates as O-GlcNAc Transferase Inhibitors.
Authors: Rafie, K. / Gorelik, A. / Trapannone, R. / Borodkin, V.S. / van Aalten, D.M.F.
History
DepositionApr 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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
E: bisubstrate inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6754
Polymers81,1902
Non-polymers4852
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-8 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.038, 150.951, 200.540
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-1274-

HOH

21A-1325-

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 / OGT


Mass: 80475.945 Da / Num. of mol.: 1 / Fragment: UNP residues 325-1041
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide bisubstrate inhibitor


Mass: 713.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-94T / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] propyl hydrogen phosphate


Mass: 446.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2O12P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.33 Å3/Da / Density % sol: 63 % / Description: tetragonal
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Reservoir solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol Drop solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol, 0.5 M (NH4)2SO4, crystal seeds Seeds were generated from crystals grown in 1.3 M ...Details: Reservoir solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol Drop solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol, 0.5 M (NH4)2SO4, crystal seeds Seeds were generated from crystals grown in 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→46.01 Å / Num. obs: 88158 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.048 / Rsym value: 0.078 / Net I/σ(I): 9.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.65 / Rpim(I) all: 0.711 / Rsym value: 1.202 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimless0.5.15data scaling
MOLREP11.4.03phasing
Coot0.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE4

3pe4


Resolution: 1.85→46.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.383 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23641 4369 5 %RANDOM
Rwork0.20497 ---
obs0.2065 83781 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20 Å2
2--4.54 Å20 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.85→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5564 0 1 362 5927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195706
X-RAY DIFFRACTIONr_bond_other_d0.0020.025459
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9687747
X-RAY DIFFRACTIONr_angle_other_deg0.9683.00512567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60524.559261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49215972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3111530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216443
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021302
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_it2.4994.462786
X-RAY DIFFRACTIONr_mcbond_other2.4984.4622787
X-RAY DIFFRACTIONr_mcangle_it3.7216.6763479
X-RAY DIFFRACTIONr_mcangle_other3.7236.6773480
X-RAY DIFFRACTIONr_scbond_it2.9124.7952917
X-RAY DIFFRACTIONr_scbond_other2.9124.7972918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.747.0634269
X-RAY DIFFRACTIONr_long_range_B_refined6.53453.2116435
X-RAY DIFFRACTIONr_long_range_B_other6.46653.0516372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 304 -
Rwork0.393 6185 -
obs--99.83 %

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