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- PDB-6ma1: Crystal structure of human O-GlcNAc transferase bound to a peptid... -

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Basic information

Entry
Database: PDB / ID: 6ma1
TitleCrystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor 4a
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 / 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 / histone methyltransferase complex / regulation of synapse assembly / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / MLL1 complex / hemopoiesis / histone acetyltransferase complex / mitophagy / regulation of protein-containing complex assembly / positive regulation of cell cycle / positive regulation of lipid biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / negative regulation of cell migration / cell projection / positive regulation of translation / cellular response to glucose stimulus / mitochondrial membrane / 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 / chromatin DNA binding / protein processing / UCH proteinases / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / transcription coactivator activity / protein stabilization / cadherin binding / chromatin remodeling / neuronal cell body / glutamatergic synapse / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / apoptotic process / 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 / identical protein binding / membrane / 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 ...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 / 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-JA4 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Host cell factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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)83,1593
Polymers82,5832
Non-polymers5761
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-0 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.303, 100.303, 130.301
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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-JA4 / N-[(2R)-2-{[(7-chloro-2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}-2-(2-methoxyphenyl)acetyl]-N-[(thiophen-2-yl)methyl]glycine


Mass: 576.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22ClN3O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.1 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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→50.15 Å / Num. obs: 20214 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 64.39 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.082 / Rrim(I) all: 0.226 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.96.71.53929030.2480.6281.66599.8
8.7-50.157.10.0767100.9960.030.08299.5

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N39

4n39


Resolution: 2.75→46.804 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.6
RfactorNum. reflection% reflection
Rfree0.2403 1040 5.15 %
Rwork0.199 --
obs0.2011 20180 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.97 Å2 / Biso mean: 73.9031 Å2 / Biso min: 36.12 Å2
Refinement stepCycle: final / Resolution: 2.75→46.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 59 41 5676
Biso mean--70.74 54.13 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025756
X-RAY DIFFRACTIONf_angle_d0.4227814
X-RAY DIFFRACTIONf_chiral_restr0.038863
X-RAY DIFFRACTIONf_plane_restr0.0021015
X-RAY DIFFRACTIONf_dihedral_angle_d12.4613485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.75-2.8950.3891460.344126962842
2.895-3.07630.32171500.300126702820
3.0763-3.31380.33261460.254927052851
3.3138-3.64710.25551680.219227022870
3.6471-4.17460.20051490.176327282877
4.1746-5.25840.1881320.166327572889
5.2584-46.8110.22281490.164328823031
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)
11.6584-0.2583-0.44481.27510.1433.35890.34980.1640.3857-0.2805-0.01620.1062-1.14290.1718-0.59920.8303-0.07220.09420.63080.02060.9133-44.860234.341129.4386
22.9021-0.5275-0.48462.06040.62492.24140.2822-0.10480.25870.287-0.0806-0.41730.2570.202-0.2850.6088-0.013-0.02090.5701-0.01270.5627-40.403224.312634.9962
32.21.08110.5061.75970.51442.5060.3790.0643-0.5067-0.0682-0.0965-0.2030.0581-0.1438-0.19280.64040.03910.01430.51650.00180.5431-46.060211.240227.6277
41.1434-0.2108-1.26881.95220.4962.1604-0.27250.0553-0.1076-0.03080.20510.09530.179-0.30150.12920.62070.02140.01610.6070.06830.4428-52.26219.390610.5561
52.83990.42380.56482.3289-0.63192.01210.08180.14210.0144-0.26450.2336-0.2091-0.1956-0.0156-0.27760.6039-0.05380.02930.6739-0.02340.5142-45.100222.02544.5253
60.86930.63340.10611.26820.14511.8404-0.179-0.25370.31520.18590.3902-0.81680.05730.4731-0.21410.53960.0538-0.15430.8237-0.25861.0071-17.239716.43479.5178
72.56510.1692-0.10842.6142-0.46460.99040.0762-0.06350.5677-0.57650.2564-0.6455-0.16690.322-0.36440.6157-0.05720.09780.6215-0.14780.6303-25.986615.0562-5.7107
82.0038-1.3888-0.66662.3827-0.73751.3943-0.36890.0582-0.00220.33320.09010.16630.4007-0.00070.32710.91560.00680.16190.5827-0.19020.695-23.9489-20.9855-15.0728
93.5129-0.7762-0.31923.4789-0.65415.62770.5850.5215-0.6552-0.07030.5480.66270.1422-0.1168-1.04940.88710.04950.04570.6861-0.10940.9646-27.1361-24.8594-13.0589
101.8275-0.4536-0.08592.39180.01581.3252-0.13490.123-0.0999-0.06360.1045-0.38060.44790.28450.03860.67710.09420.06190.6087-0.09550.5952-31.5146-12.8181-3.2446
112.65890.00460.6641.8058-1.14352.1819-0.02090.1070.18470.02260.04320.3282-0.1629-0.08250.17680.6527-0.0703-0.02460.51070.02410.5606-47.0598-4.8989-7.6704
121.6038-0.5025-0.01773.785-0.50781.5581-0.11290.2994-0.0012-0.49780.2096-0.25980.1908-0.0218-0.05250.6421-0.07330.06930.5307-0.07970.3964-35.0288-0.1248-12.7091
133.8542-1.81890.31724.9892-0.33561.736-0.30720.2790.8739-0.65370.6976-2.5403-0.5720.7791-0.48910.6312-0.09580.0850.7831-0.24931.1675-15.090525.1996-6.3806
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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