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- PDB-5vif: Electrophilic probes for deciphering substrate recognition by O-G... -

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Basic information

Entry
Database: PDB / ID: 5vif
TitleElectrophilic probes for deciphering substrate recognition by O-GlcNAc transferase
Components
  • CKIICrusader Kings II
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / O-GlcNAc Transferase / Glycosylation Electrophilic Probes / CKII
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 chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / : / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / Receptor Mediated Mitophagy / Sin3-type complex / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / mitophagy / negative regulation of apoptotic signaling pathway / hemopoiesis / positive regulation of Wnt signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / chaperone-mediated protein folding / positive regulation of lipid biosynthetic process / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / negative regulation of cell migration / positive regulation of translation / Signal transduction by L1 / cell projection / cellular response to glucose stimulus / mitochondrial membrane / negative regulation of transforming growth factor beta receptor signaling pathway / peptidyl-threonine phosphorylation / Hsp90 protein binding / circadian regulation of gene expression / response to insulin / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / PML body / protein processing / chromatin DNA binding / Wnt signaling pathway / Regulation of PTEN stability and activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / UCH proteinases / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / positive regulation of cold-induced thermogenesis / chromatin organization / kinase activity / HATs acetylate histones / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / protein stabilization / regulation of cell cycle / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / DNA damage response / positive regulation of cell population proliferation / 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 / ATP binding / identical protein binding / 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 / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-9C1 / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJiang, J. / Li, B. / Hu, C.-W. / Worth, M. / Fan, D. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Wisconsin-Madison United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase.
Authors: Hu, C.W. / Worth, M. / Fan, D. / Li, B. / Li, H. / Lu, L. / Zhong, X. / Lin, Z. / Wei, L. / Ge, Y. / Li, L. / Jiang, J.
History
DepositionApr 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
B: CKII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0594
Polymers82,3732
Non-polymers6862
Water3,441191
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: CKII
hetero molecules

A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: CKII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,1188
Polymers164,7464
Non-polymers1,3724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
Buried area9660 Å2
ΔGint-60 kcal/mol
Surface area51690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.084, 152.733, 199.398
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-1250-

HOH

21A-1270-

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: 80974.508 Da / Num. of mol.: 1 / Fragment: UNP residues 323-1041
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: Protein/peptide CKII / Crusader Kings II


Mass: 1398.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68400*PLUS
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Sugar ChemComp-9C1 / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucose / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-D-glucose / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 281.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16ClNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.08 M BIS-TRIS propane (pH 7.0), 0.02 M sodium cacodylate trihydrate (pH 6.5), 2.8 M sodium formate, 0.04 M ammonium sulfate, and 6% w/v polyethylene glycol 8,000.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→50.01 Å / Num. obs: 58556 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Net I/σ(I): 40.8
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / Num. unique obs: 2858 / CC1/2: 0.963 / Rpim(I) all: 0.157 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE3

3pe3


Resolution: 2.25→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.372 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22849 2558 5.1 %RANDOM
Rwork0.18175 ---
obs0.18424 47541 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å20 Å2
2--6.56 Å20 Å2
3----4.01 Å2
Refinement stepCycle: 1 / Resolution: 2.25→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5481 0 42 191 5714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9627734
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78324.466262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93815969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1521531
X-RAY DIFFRACTIONr_chiral_restr0.1410.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214324
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.0975.1382790
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.0237.6763484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0095.572901
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.85648.32124967
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 176 -
Rwork0.283 3485 -
obs--100 %

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