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- PDB-6ma2: Crystal structure of human O-GlcNAc transferase bound to a peptid... -

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Basic information

Entry
Database: PDB / ID: 6ma2
TitleCrystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor ent-1a
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


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / release from viral latency / 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 non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / release from viral latency / 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 / blastocyst hatching / negative regulation of stem cell population maintenance / protein O-linked glycosylation / Set1C/COMPASS complex / MLL1/2 complex / 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 / histone methyltransferase complex / hemopoiesis / MLL1 complex / positive regulation of proteolysis / histone acetyltransferase complex / regulation of protein-containing complex assembly / positive regulation of lipid biosynthetic process / mitophagy / positive regulation of cell cycle / 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 / Transcriptional activation of mitochondrial biogenesis / 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 / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / transcription coactivator activity / protein stabilization / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / neuronal cell body / apoptotic process / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / 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 / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Host cell factor / Host cell factor, Kelch-repeats domain / 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 ...Host cell factor / Host cell factor, Kelch-repeats domain / 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 / Kelch-type beta propeller / Tetratricopeptide repeat / Glycogen Phosphorylase B; / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J9S / 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: 2.1 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)83,1253
Polymers82,5832
Non-polymers5421
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint0 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.610, 98.610, 365.111
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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-J9S / N-[(2S)-2-(2-methoxyphenyl)-2-{[(2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}acetyl]-N-[(thiophen-2-yl)methyl]glycine


Mass: 541.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23N3O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.1 Å3/Da / Density % sol: 60.36 % / Mosaicity: 0.25 °
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-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→91.28 Å / Num. obs: 62582 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.072 / Rrim(I) all: 0.203 / Net I/σ(I): 6.2 / Num. measured all: 483344 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.6 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.151.2344990.5710.5111.33599.8
9.39-91.280.0798900.9940.0320.085100

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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: 2.1→85.399 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.218 3120 5 %
Rwork0.1853 --
obs0.187 62340 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.85 Å2 / Biso mean: 38.0775 Å2 / Biso min: 18.22 Å2
Refinement stepCycle: final / Resolution: 2.1→85.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 59 298 5962
Biso mean--59.41 36.21 -
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085785
X-RAY DIFFRACTIONf_angle_d0.8087854
X-RAY DIFFRACTIONf_chiral_restr0.051869
X-RAY DIFFRACTIONf_plane_restr0.0061020
X-RAY DIFFRACTIONf_dihedral_angle_d12.6073501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13280.31311490.27092599274899
2.1328-2.16780.32111370.2642606274399
2.1678-2.20520.27231380.244826212759100
2.2052-2.24530.27471210.236226812802100
2.2453-2.28850.26041300.220326392769100
2.2885-2.33520.26751460.220526142760100
2.3352-2.3860.26381370.210826422779100
2.386-2.44150.26651570.196126422799100
2.4415-2.50250.22811440.198726312775100
2.5025-2.57020.2191270.201826542781100
2.5702-2.64580.23631330.210126852818100
2.6458-2.73120.2391430.211626672810100
2.7312-2.82890.24331380.220726762814100
2.8289-2.94210.27861250.217526902815100
2.9421-3.0760.23941600.210226872847100
3.076-3.23820.22091370.211226712808100
3.2382-3.44110.22421400.189727342874100
3.4411-3.70680.20881410.173727202861100
3.7068-4.07980.2061470.146327552902100
4.0798-4.67020.15551550.127827592914100
4.6702-5.88370.1651650.149928042969100
5.8837-85.46960.19221500.171530433193100
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)
13.8126-0.38772.2328.1744-3.9873.6186-0.0006-0.05790.19850.29430.17880.1292-0.5165-0.3306-0.22020.35460.09320.05080.3917-0.12020.3258-16.749-38.66756.505
22.84580.6703-0.15575.3199-1.91991.3117-0.0319-0.33210.07170.31550.0620.0952-0.0804-0.1175-0.00640.20410.03090.00130.3247-0.07080.2089-7.317-46.90855.222
31.3011-0.00021.90245.7063-0.87497.1632-0.1004-0.15650.1260.14080.1102-0.10790.1076-0.2601-0.01150.12440.01120.01670.235-0.03070.2147-9.437-55.55141.694
40.2122-0.5656-0.09293.2703-0.77095.73610.00940.10010.149-0.14760.11140.0329-0.0693-0.62-0.09820.1455-0.0170.01590.37080.02430.2668-19.154-51.69526.673
54.52222.98452.33068.18881.07193.4720.1236-0.10020.25610.1581-0.0380.1789-0.2816-0.4676-0.07990.20080.09080.03410.36420.02650.2702-19.747-36.01328.881
61.1669-0.3581-0.09480.7083-0.04141.77470.0752-0.17050.28610.13650.0351-0.237-0.4660.4595-0.0930.3035-0.1023-0.00360.2967-0.04360.33118.239-28.19629.812
71.9642-1.4498-2.7322.83822.47246.22830.26020.07580.4206-0.15260.0133-0.0948-0.7755-0.1881-0.26340.2855-0.01360.02030.23770.03140.319-3.251-26.23816.589
86.717-1.2443-4.24235.3607-1.35763.5831-0.1180.4732-0.2093-0.3232-0.0092-0.08640.00170.60730.12290.2404-0.03520.0230.53520.01910.23310.897-46.588-11.812
98.20243.6705-1.46288.2132-5.7039.47870.22120.8009-0.1031-0.38790.05470.45460.2630.0028-0.2680.2512-0.02640.01660.4626-0.1280.323610.337-52.029-12.198
108.5801-0.5447-0.50140.68750.04721.1716-0.06440.0787-0.0761-0.04380.0045-0.05390.01270.07370.05370.1782-0.03390.01690.19630.0470.21694.13-50.1562.742
114.964-1.85752.34854.8802-3.26734.2441-0.11930.32150.013-0.23350.27010.23310.1611-0.5991-0.15050.1717-0.06260.00170.3522-0.00490.2295-14.029-50.043.17
121.4519-0.33550.15381.1327-0.05842.7330.04540.20780.109-0.08450.00620.0664-0.1941-0.3155-0.03840.1623-0.00260.0120.32720.06350.2504-6.805-37.9991.971
137.5593-1.8727-0.18528.45665.22233.35460.17340.48161.1312-0.15360.0719-0.034-1.45320.1062-0.16560.7641-0.09570.02780.25250.09480.55211.788-13.09521.852
142.26912.9279-3.62944.9845-5.10995.9547-0.8630.8026-0.2357-0.33721.70852.25632.2869-3.1999-0.81140.4499-0.21090.06420.55620.09870.5248-22.289-49.19257.169
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
14X-RAY DIFFRACTION14( CHAIN B AND RESID 22:24 )B22 - 24

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