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- PDB-6ma4: Crystal structure of human O-GlcNAc transferase bound to a peptid... -

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Basic information

Entry
Database: PDB / ID: 6ma4
TitleCrystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor 3a
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-JA7 / 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)83,2113
Polymers82,5832
Non-polymers6281
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-0 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.630, 98.630, 365.202
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-1406-

HOH

21A-1566-

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-JA7 / 5-{2-[(1R)-2-{(carboxymethyl)[(thiophen-2-yl)methyl]amino}-2-oxo-1-{[(2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}ethyl]phenoxy}pentanoic acid


Mass: 627.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H29N3O9S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 60.38 % / Mosaicity: 0.55 °
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: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→77.37 Å / Num. obs: 70941 / % possible obs: 98.7 % / Redundancy: 4.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.087 / Rrim(I) all: 0.198 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.045.11.05844770.4890.5121.17998.6
9.59-77.374.10.0537870.9970.0260.0695.4

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4N3A

4n3a


Resolution: 2→77.37 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.34
RfactorNum. reflection% reflection
Rfree0.2204 3542 5 %
Rwork0.1908 --
obs0.1923 70836 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.43 Å2 / Biso mean: 34.6358 Å2 / Biso min: 15.35 Å2
Refinement stepCycle: final / Resolution: 2→77.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5611 0 70 401 6082
Biso mean--54.2 35.81 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045795
X-RAY DIFFRACTIONf_angle_d0.6037867
X-RAY DIFFRACTIONf_chiral_restr0.044871
X-RAY DIFFRACTIONf_plane_restr0.0041021
X-RAY DIFFRACTIONf_dihedral_angle_d12.5643510
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 (%)
2-2.02740.30361200.29922646276698
2.0274-2.05640.361520.2872661281398
2.0564-2.08710.32251330.28192604273798
2.0871-2.11970.29051420.25842603274598
2.1197-2.15440.30581390.25342625276497
2.1544-2.19160.25921410.24792680282198
2.1916-2.23140.29021320.24022597272998
2.2314-2.27440.28811210.22672616273797
2.2744-2.32080.281420.22172645278799
2.3208-2.37130.24881490.21782672282198
2.3713-2.42640.27451360.20882654279099
2.4264-2.48710.29121670.20622642280998
2.4871-2.55440.22131220.21322663278598
2.5544-2.62950.23281310.20222696282799
2.6295-2.71440.20091400.20012690283099
2.7144-2.81140.251490.21142640278997
2.8114-2.9240.23491220.20692697281998
2.924-3.05710.22341690.20542678284798
3.0571-3.21830.22681380.20712721285999
3.2183-3.41990.221350.18322774290999
3.4199-3.68390.2121400.17522695283598
3.6839-4.05460.18431530.147827872940100
4.0546-4.64130.17541550.13062798295399
4.6413-5.84730.16331680.15082803297198
5.8473-77.42760.16471460.17283007315397
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)
17.883-0.3140.18797.3533-2.50225.6958-0.0009-0.12640.31030.04940.12270.0629-0.4631-0.2558-0.120.27780.08330.06390.3145-0.11410.236-16.7219-38.756556.4513
21.8261.34770.04383.9824-1.95642.3918-0.0163-0.32180.07170.22490.0164-0.0132-0.1540.0119-0.00420.16170.03440.0130.3061-0.05470.184-7.4816-46.951855.1732
30.9945-0.23481.53344.4665-0.68636.029-0.0984-0.14080.16090.10060.0959-0.13350.0426-0.16360.00370.09750.01290.00530.2177-0.02880.1827-9.6022-55.647741.6709
40.1627-0.4733-0.16623.1089-0.675.6981-0.05040.00650.0829-0.10540.12660.0691-0.0756-0.4538-0.07770.1104-0.0160.00640.28760.0110.2017-19.3779-51.804726.7228
55.26022.43071.4785.80660.84842.95210.0699-0.06380.21180.14010.04760.2778-0.3187-0.3623-0.12730.18410.10840.03190.28890.01390.2243-19.9811-36.117628.9342
60.9489-0.3228-0.03720.8873-0.05841.83460.0615-0.1930.22010.12960.0237-0.1944-0.47580.4334-0.08040.2858-0.10450.00450.2815-0.05360.28758.0269-28.334529.8299
71.4772-0.9161-1.88492.89171.5835.04050.16020.08780.3342-0.02590.06020.0204-0.7053-0.1603-0.2120.25740.00060.0170.19310.02380.231-3.4745-26.287116.6283
87.4003-1.367-3.84834.2883-1.23582.9632-0.08580.337-0.1794-0.301-0.0894-0.1605-0.02030.52410.15820.2354-0.0360.03820.44510.01350.215710.6384-46.5566-11.8178
97.8781.7866-0.90423.5839-4.2955.83160.12850.7499-0.2799-0.2134-0.25960.00990.22680.02350.10630.2675-0.03090.02040.3685-0.12540.228810.1572-51.9922-12.2364
105.6718-0.2175-0.77240.72130.11631.9145-0.0480.1751-0.1015-0.05860.005-0.079-0.00250.08290.04110.1572-0.02910.01620.15010.03420.19453.9102-50.18372.7202
114.2225-1.65261.21994.9917-3.39133.7981-0.12950.4338-0.0162-0.29150.21250.13870.3345-0.6361-0.07390.1566-0.063-0.00920.29980.00270.1692-14.1963-50.04513.2575
121.9759-0.1801-0.00450.9237-0.3682.68980.02270.17550.0752-0.14320.04440.0609-0.2207-0.3233-0.04070.15910.01730.0070.25080.0440.1957-7.0411-38.06892.0121
136.0835-1.77140.14896.41634.07882.88820.13240.45730.9416-0.17730.174-0.0067-1.70140.35-0.210.8565-0.07170.08610.18860.05480.471.545-13.169821.9246
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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