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- PDB-6ma3: Crystal structure of human O-GlcNAc transferase bound to a peptid... -

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Basic information

Entry
Database: PDB / ID: 6ma3
TitleCrystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor 2a
Components
  • Host Cell Factor 1 peptide
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Keywordstransferase/transferase inhibitor / OGT / O-GlcNAc / glycosyltransferase / enzyme-inhibitor complex / transferase-transferase inhibitor complex
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / release from viral latency / 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 N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / release from viral latency / 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 / Set1C/COMPASS complex / MLL1/2 complex / NSL complex / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / histone methyltransferase complex / 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 / MLL1 complex / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / regulation of protein-containing complex assembly / positive regulation of cell cycle / 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 / Transcriptional activation of mitochondrial biogenesis / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / protein-macromolecule adaptor activity / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / protein stabilization / chromatin remodeling / cadherin binding / cell cycle / neuronal cell body / glutamatergic synapse / apoptotic process / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / 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 / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Host cell factor / Kelch motif / Galactose oxidase, central domain / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Kelch repeat type 1 / Kelch motif / Tetratricopeptide repeat 1 ...Host cell factor / Kelch motif / Galactose oxidase, central domain / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Kelch repeat type 1 / Kelch motif / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Kelch-type beta propeller / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tetratricopeptide-like helical domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-JAJ / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Host cell factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsMartin, S.E.S. / Lazarus, M.B. / Walker, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094263 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors.
Authors: Martin, S.E.S. / Tan, Z.W. / Itkonen, H.M. / Duveau, D.Y. / Paulo, J.A. / Janetzko, J. / Boutz, P.L. / Tork, L. / Moss, F.A. / Thomas, C.J. / Gygi, S.P. / Lazarus, M.B. / Walker, S.
History
DepositionAug 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 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_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
B: Host Cell Factor 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1973
Polymers82,5832
Non-polymers6141
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-1 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.180, 98.180, 365.104
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1315-

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Plasmid: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide Host Cell Factor 1 peptide


Mass: 1608.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51610*PLUS
#3: Chemical ChemComp-JAJ / 4-{2-[(1R)-2-{(carboxymethyl)[(thiophen-2-yl)methyl]amino}-2-oxo-1-{[(2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}ethyl]phenoxy}butanoic acid


Mass: 613.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27N3O9S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 3.08 Å3/Da / Density % sol: 60.01 % / Mosaicity: 0.31 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.05 M Sodium Citrate Tribasic Dihydrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→85.03 Å / Num. obs: 70965 / % possible obs: 99.3 % / Redundancy: 5.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.067 / Rrim(I) all: 0.165 / Net I/σ(I): 6.7 / Num. measured all: 399210 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.044.21.25144040.4690.661.42397.5
9.59-85.034.60.0418090.9980.0210.04696.6

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4N3A

4n3a


Resolution: 2→85.026 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2117 3542 5.01 %
Rwork0.1858 --
obs0.1871 70760 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.02 Å2 / Biso mean: 35.7646 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 2→85.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 67 350 6015
Biso mean--30.5 37.39 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035790
X-RAY DIFFRACTIONf_angle_d0.5377860
X-RAY DIFFRACTIONf_chiral_restr0.042869
X-RAY DIFFRACTIONf_plane_restr0.0041021
X-RAY DIFFRACTIONf_dihedral_angle_d12.3013505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02740.3361510.31092549270097
2.0274-2.05640.33291360.29242551268796
2.0564-2.08710.27951440.28212593273797
2.0871-2.11970.29971350.25282622275799
2.1197-2.15450.2861390.24562650278999
2.1545-2.19160.25821250.237826542779100
2.1916-2.23150.26931450.223226922837100
2.2315-2.27440.25821500.213526472797100
2.2744-2.32080.23041410.21252627276899
2.3208-2.37130.21271350.211226732808100
2.3713-2.42650.26311270.20872673280099
2.4265-2.48720.22831380.198126672805100
2.4872-2.55440.2431710.204726502821100
2.5544-2.62960.24621260.204727142840100
2.6296-2.71450.21681650.197926652830100
2.7145-2.81150.24171320.21012696282899
2.8115-2.92410.23821200.20932692281299
2.9241-3.05710.22091370.19432706284399
3.0571-3.21830.20391350.201527192854100
3.2183-3.420.21071410.18322728286999
3.42-3.6840.19251480.16212713286199
3.684-4.05480.16481340.14182743287798
4.0548-4.64150.14441530.130827912944100
4.6415-5.84750.19761500.14972786293698
5.8475-85.10320.18631640.1733017318198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.0209-0.53880.52126.6075-2.33514.42840.19140.0610.35440.24250.10850.1247-0.5334-0.1657-0.24190.36890.03510.12360.3414-0.14280.2791-16.621-38.42756.381
22.03950.91070.55253.8986-1.80551.6035-0.0137-0.26070.01180.2799-0.05250.0097-0.1642-0.0030.07240.17290.00570.02920.2849-0.08090.1901-7.376-46.44854.844
31.7359-0.61881.52914.8806-0.4485.9935-0.0826-0.03440.10090.0140.0387-0.11470.063-0.12940.03760.0972-0.01850.02060.2423-0.04380.1753-9.511-55.28941.598
40.3552-0.3677-0.30882.6846-0.53134.0337-0.03650.08340.0922-0.05530.08570.1042-0.0136-0.6015-0.03640.1169-0.0320.01170.3738-0.01740.2272-19.317-51.53926.715
54.29622.61621.47526.2123-0.51741.24070.071-0.16810.30040.2631-0.00830.2625-0.3055-0.4157-0.07040.19430.110.03020.43-0.02880.2519-19.837-35.82628.877
61.0887-0.17150.13761.17650.14721.48570.092-0.16050.23430.12390.0411-0.1802-0.45290.4141-0.08470.3107-0.1070.0160.2823-0.0730.31418.181-28.06429.694
71.0857-0.9012-1.34892.97791.78255.1480.18580.06410.34-0.11410.0050.011-0.7756-0.3446-0.16250.28710.0170.02930.2376-0.00150.2999-3.305-26.09916.499
85.9397-0.1052-3.61213.3333-0.76872.4049-0.12530.708-0.0717-0.4052-0.0491-0.10110.00060.57030.13840.2475-0.030.0440.5638-0.00120.229310.73-46.523-11.797
97.1022.2596-1.66339.0948-5.56616.19630.27890.86-0.262-0.3845-0.10310.15570.14280.0466-0.26680.3127-0.0179-0.01210.4519-0.19550.302710.213-51.948-12.367
106.2291-0.4829-0.5670.60690.40721.9969-0.01540.0627-0.1193-0.08890.0242-0.07100.0821-0.00090.1554-0.0450.02440.16610.01660.20574.008-50.0392.767
113.7951-1.41082.09034.7333-2.4372.4563-0.03850.3649-0.1205-0.25980.17910.24450.1374-0.5539-0.15340.1381-0.04360.00050.3795-0.01270.2008-14.125-49.9143.401
121.5685-0.2098-0.01531.22510.00432.65950.03040.16190.1013-0.18620.00480.0565-0.2674-0.3409-0.02820.17110.01310.01310.27470.02040.2089-6.856-37.9552.004
135.7741-2.0458-0.25017.9375.55624.15510.04330.27540.7828-0.2820.0727-0.0788-1.48320.1662-0.19690.7726-0.07260.03760.2350.03780.47771.793-13.01221.727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 313:341 )A313 - 341
2X-RAY DIFFRACTION2( CHAIN A AND RESID 342:382 )A342 - 382
3X-RAY DIFFRACTION3( CHAIN A AND RESID 383:429 )A383 - 429
4X-RAY DIFFRACTION4( CHAIN A AND RESID 430:474 )A430 - 474
5X-RAY DIFFRACTION5( CHAIN A AND RESID 475:518 )A475 - 518
6X-RAY DIFFRACTION6( CHAIN A AND RESID 519:654 )A519 - 654
7X-RAY DIFFRACTION7( CHAIN A AND RESID 655:706 )A655 - 706
8X-RAY DIFFRACTION8( CHAIN A AND RESID 707:742 )A707 - 742
9X-RAY DIFFRACTION9( CHAIN A AND RESID 743:784 )A743 - 784
10X-RAY DIFFRACTION10( CHAIN A AND RESID 785:849 )A785 - 849
11X-RAY DIFFRACTION11( CHAIN A AND RESID 850:876 )A850 - 876
12X-RAY DIFFRACTION12( CHAIN A AND RESID 877:1003 )A877 - 1003
13X-RAY DIFFRACTION13( CHAIN A AND RESID 1004:1028 )A1004 - 1028

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