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- PDB-3pe3: Structure of human O-GlcNAc transferase and its complex with a pe... -

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Basic information

Entry
Database: PDB / ID: 3pe3
TitleStructure of human O-GlcNAc transferase and its complex with a peptide substrate
ComponentsUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / GT-B / glycosyltransferase
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / 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 ...protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / 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 / NSL complex / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of proteolysis / mitophagy / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / 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 / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / chromatin organization / positive regulation of cold-induced thermogenesis / HATs acetylate histones / glutamatergic synapse / apoptotic process / 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 / nucleus / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.78 Å
AuthorsLazarus, M.B. / Nam, Y. / Jiang, J. / Sliz, P. / Walker, S.
CitationJournal: Nature / Year: 2011
Title: Structure of human O-GlcNAc transferase and its complex with a peptide substrate.
Authors: Lazarus, M.B. / Nam, Y. / Jiang, J. / Sliz, P. / Walker, S.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 21, 2021Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,5158
Polymers323,8984
Non-polymers1,6174
Water4,774265
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3792
Polymers80,9751
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3792
Polymers80,9751
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3792
Polymers80,9751
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3792
Polymers80,9751
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.4, 273.4, 142.8
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number150
Space group name H-MP321

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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


Mass: 80974.508 Da / Num. of mol.: 4 / Fragment: hOGT4.5, UNP residues 323-1041
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, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 4.76 Å3/Da / Density % sol: 74.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.45 M Potassium Phosphate Dibasic, 8 mM EDTA, 1% xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. all: 157058 / Num. obs: 154231 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.116 / Net I/σ(I): 8.4
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.425 / % possible all: 95.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.78→48.583 Å / SU ML: 0.38 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 2024 1.34 %RANDOM
Rwork0.1847 ---
obs0.1852 151013 97.82 %-
all-154378 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.964 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 49.749 Å2
Baniso -1Baniso -2Baniso -3
1--0.2264 Å20 Å2-0 Å2
2---0.2264 Å2-0 Å2
3----16.1612 Å2
Refinement stepCycle: LAST / Resolution: 2.78→48.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22136 0 100 265 22501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322748
X-RAY DIFFRACTIONf_angle_d0.70730864
X-RAY DIFFRACTIONf_dihedral_angle_d13.7468524
X-RAY DIFFRACTIONf_chiral_restr0.0483408
X-RAY DIFFRACTIONf_plane_restr0.0034004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.84480.31731120.27719874X-RAY DIFFRACTION91
2.8448-2.92170.31281330.257410428X-RAY DIFFRACTION96
2.9217-3.00770.27671380.248210533X-RAY DIFFRACTION97
3.0077-3.10470.25621500.245710584X-RAY DIFFRACTION98
3.1047-3.21570.27221230.235510688X-RAY DIFFRACTION98
3.2157-3.34440.26311700.218510604X-RAY DIFFRACTION98
3.3444-3.49660.24581470.198510642X-RAY DIFFRACTION98
3.4966-3.68080.21631610.174210697X-RAY DIFFRACTION99
3.6808-3.91140.19031430.157410747X-RAY DIFFRACTION99
3.9114-4.21320.19681400.142810777X-RAY DIFFRACTION99
4.2132-4.63690.1761440.134110797X-RAY DIFFRACTION99
4.6369-5.30720.18231460.127610782X-RAY DIFFRACTION99
5.3072-6.68370.16951570.145110848X-RAY DIFFRACTION99
6.6837-48.59070.17051600.171210988X-RAY DIFFRACTION98
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)
10.0651-0.00620.05910.04580.02740.31110.0538-0.286-0.1075-0.0997-0.0104-0.0519-0.0722-0.3761-0.00390.623-0.2369-0.06620.60950.21940.4765-31.6118173.344934.484
20.41470.15720.25150.23190.03770.3366-0.0943-0.1319-0.1224-0.23810.0867-0.0088-0.0476-0.17940.01070.45670.0210.02750.10420.03530.1271-24.2276197.461730.0609
30.32440.26090.29510.59840.14460.15880.0211-0.36190.06790.17110.3064-0.18270.02310.233-0.04750.37440.2268-0.0352-1.25940.37990.01332.9268195.916241.6818
40.1505-0.0068-0.08360.38170.02380.2080.02290.20740.1534-0.04960.0907-0.2696-0.26310.1618-0.06110.48930.03660.0499-0.11750.01120.24787.3961227.258228.0607
50.07320.26870.18850.232-0.01160.2195-0.0634-0.03390.11710.06720.0772-0.0911-0.2137-0.0108-0.03050.50690.1272-0.01070.0331-0.02570.17680.9013217.864344.134
60.0350.02670.01650.2252-0.17660.22680.189-0.08080.14930.09680.125-0.019-0.24310.3414-0.01850.7044-0.2824-0.05390.45380.02120.32132.0272210.56376.6214
70.3347-0.08190.27090.00170.04010.47710.042-0.1146-0.05450.09570.04230.0105-0.3499-0.0215-0.07640.55310.00080.02890.0987-0.00920.1956-22.1582212.6351-1.2991
80.27830.04910.00550.1652-0.03370.42680.0675-0.0290.06630.1262-0.04690.0768-0.2044-0.0404-0.02030.3233-0.01340.022-0.00780.01320.1291-17.2012212.486-30.4668
90.25970.027-0.0910.54420.17190.3140.06280.0632-0.02760.1042-0.05280.1216-0.1234-0.2623-0.03430.26560.12380.04970.21620.00970.1481-51.515210.8147-33.4267
100.18410.0363-0.12780.0272-0.26130.1080.0523-0.00330.2055-0.0120.0034-0.0227-0.3029-0.2652-0.08070.45350.12170.11210.02410.01530.1867-36.4567223.42-31.7281
110.18050.04050.05090.0767-0.00220.0226-0.05590.17380.055-0.37290.12310.19460.11250.07210.01480.6721-0.1392-0.15910.61860.19170.4592-44.1409188.2599-19.4806
120.250.18070.03950.3517-0.29030.82210.06840.04420.1721-0.19080.13370.2706-0.10510.0365-0.17130.38120.0103-0.03260.19480.06090.3083-48.2266190.53425.5898
130.11750.10060.12290.4845-0.06260.3403-0.1027-0.00580.0775-0.12750.13520.18320.0448-0.1846-0.04270.1159-0.1256-0.07230.18720.07330.1309-59.4967163.653710.5273
140.3282-0.15440.07770.2175-0.07510.40250.0362-0.13810.15740.1449-0.0562-0.0102-0.1645-0.14330.00350.3907-0.07050.13820.292-0.04250.2934-57.4335172.296643.8825
150.2696-0.0224-0.22870.3447-0.06930.68710.0004-0.14460.05920.07380.10360.3865-0.0996-0.2987-0.08910.26060.01110.08340.3006-0.00740.5152-69.1732173.258628.036
160.5515-0.12820.07660.0714-0.00760.068-0.13460.2342-0.21640.1617-0.18480.5144-0.0094-0.05610.08210.2565-0.085-0.01470.4295-0.10590.9055-26.817138.360492.6763
170.0906-0.0389-0.04090.6209-0.23130.14580.0324-0.0123-0.0696-0.1143-0.12140.03650.0734-0.05040.07320.2004-0.0896-0.00480.1398-0.01990.1711-20.0943159.434280.3339
180.2579-0.1589-0.050.14870.0750.2847-0.07190.0305-0.03460.10260.00050.06640.0538-0.11420.00860.1881-0.12530.06870.1234-0.00840.1316-39.5318178.357492.2136
190.22450.13880.13130.05820.17610.2354-0.01610.02770.00350.09850.042-0.0282-0.2767-0.0234-0.01410.36990.00040.03180.06420.02970.1052-21.4967202.461475.3978
200.35640.0119-0.03210.3778-0.04960.6150.01410.15260.0171-0.1701-0.01390.0034-0.0923-0.29650.00920.1648-0.0133-0.00090.1914-0.00870.0667-36.5528189.91973.4514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 309:349)
2X-RAY DIFFRACTION2(chain A and resid 350:514)
3X-RAY DIFFRACTION3(chain A and resid 515:714)
4X-RAY DIFFRACTION4(chain A and resid 715:875)
5X-RAY DIFFRACTION5(chain A and resid 876:1028)
6X-RAY DIFFRACTION6(chain B and resid 309:349)
7X-RAY DIFFRACTION7(chain B and resid 350:514)
8X-RAY DIFFRACTION8(chain B and resid 515:714)
9X-RAY DIFFRACTION9(chain B and resid 715:875)
10X-RAY DIFFRACTION10(chain B and resid 876:1028)
11X-RAY DIFFRACTION11(chain C and resid 309:349)
12X-RAY DIFFRACTION12(chain C and resid 350:514)
13X-RAY DIFFRACTION13(chain C and resid 515:714)
14X-RAY DIFFRACTION14(chain C and resid 715:875)
15X-RAY DIFFRACTION15(chain C and resid 876:1028)
16X-RAY DIFFRACTION16(chain D and resid 309:349)
17X-RAY DIFFRACTION17(chain D and resid 350:514)
18X-RAY DIFFRACTION18(chain D and resid 515:714)
19X-RAY DIFFRACTION19(chain D and resid 715:875)
20X-RAY DIFFRACTION20(chain D and resid 876:1028)

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