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- PDB-8fe6: Crystal structure of human O-GlcNAc transferase (OGT) in complex ... -

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Basic information

Entry
Database: PDB / ID: 8fe6
TitleCrystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide and UDP-GlcNAc
Components
  • A motif peptide
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / O-GlcNAc transferase / exosite / protein-protein interaction / complex
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 / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / mitophagy / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / response to nutrient / positive regulation of TORC1 signaling / negative regulation of cell migration / positive regulation of translation / cell projection / cellular response to glucose stimulus / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / response to insulin / mitochondrial membrane / protein processing / chromatin DNA binding / Regulation of necroptotic cell death / UCH proteinases / positive regulation of cold-induced thermogenesis / HATs acetylate histones / chromatin organization / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / glutamatergic synapse / 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
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsXie, J. / Jiang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121718 United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase.
Authors: Blankenship, C.M. / Xie, J. / Benz, C. / Wang, A. / Ivarsson, Y. / Jiang, J.
History
DepositionDec 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: A motif peptide
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: A motif peptide
E: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: A motif peptide
G: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: A motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,67512
Polymers330,2468
Non-polymers2,4294
Water00
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: A motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1693
Polymers82,5612
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-16 kcal/mol
Surface area27970 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: A motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1693
Polymers82,5612
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-15 kcal/mol
Surface area28230 Å2
MethodPISA
3
E: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: A motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1693
Polymers82,5612
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-16 kcal/mol
Surface area28270 Å2
MethodPISA
4
G: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: A motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1693
Polymers82,5612
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-15 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)281.532, 281.532, 143.212
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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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.: 4
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
A motif peptide


Mass: 1586.874 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.45M potassium phosphate, 10mM EDTA pH 8, 1% Xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127129 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127129 Å / Relative weight: 1
ReflectionResolution: 3.06→123.485 Å / Num. obs: 79618 / % possible obs: 99.7 % / Redundancy: 10.5 % / Biso Wilson estimate: 75.26 Å2 / CC1/2: 0.994 / Net I/σ(I): 12.9
Reflection shellResolution: 3.06→3.113 Å / Num. unique obs: 3990 / CC1/2: 0.492

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
Cootmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→40.64 Å / SU ML: 0.4193 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.0207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 2002 2.52 %
Rwork0.1807 77574 -
obs0.1816 79576 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.27 Å2
Refinement stepCycle: LAST / Resolution: 3.06→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22348 0 156 0 22504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002623088
X-RAY DIFFRACTIONf_angle_d0.532231356
X-RAY DIFFRACTIONf_chiral_restr0.04133468
X-RAY DIFFRACTIONf_plane_restr0.00544064
X-RAY DIFFRACTIONf_dihedral_angle_d4.56243064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.140.33171430.30825575X-RAY DIFFRACTION99.98
3.14-3.220.32651400.27765519X-RAY DIFFRACTION99.95
3.22-3.320.31151460.24745585X-RAY DIFFRACTION99.97
3.32-3.420.24381430.23015535X-RAY DIFFRACTION99.96
3.42-3.550.2671450.22015557X-RAY DIFFRACTION99.95
3.55-3.690.28091400.20325575X-RAY DIFFRACTION99.97
3.69-3.860.22461410.20085484X-RAY DIFFRACTION98.39
3.86-4.060.22311430.16755514X-RAY DIFFRACTION100
4.06-4.310.19931430.15735548X-RAY DIFFRACTION99.98
4.31-4.640.19381430.15025559X-RAY DIFFRACTION100
4.64-5.110.19341440.16165562X-RAY DIFFRACTION100
5.11-5.850.22021430.16745568X-RAY DIFFRACTION100
5.85-7.360.2111420.17795508X-RAY DIFFRACTION99.21
7.36-40.640.16021460.14235485X-RAY DIFFRACTION98.82
Refinement TLS params.Method: refined / Origin x: 43.4390963473 Å / Origin y: 39.7939926069 Å / Origin z: 62.6757461008 Å
111213212223313233
T0.56783986207 Å20.0157014240509 Å20.00918532762365 Å2-0.476004038693 Å2-0.0322175048225 Å2--0.626556181756 Å2
L0.105268463226 °20.0548711581679 °2-0.0644806306538 °2-0.0101317907314 °2-0.0181372236117 °2--0.213803970569 °2
S-0.00435081630019 Å °-0.0174494993649 Å °-0.0104052577706 Å °0.0290200887402 Å °0.00442614144023 Å °-0.0417292874122 Å °-0.0426176424312 Å °-0.0203417444093 Å °-0.000692882333467 Å °
Refinement TLS groupSelection details: all

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