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- PDB-4gz5: Crystal structure of human O-GlcNAc Transferase with UDP-GlcNAc -

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Basic information

Entry
Database: PDB / ID: 4gz5
TitleCrystal structure of human O-GlcNAc Transferase with UDP-GlcNAc
ComponentsUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / OGT / O-GlcNAc / GT-B / Glycosyltransferase / O-GlcNAcylation
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-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.075 Å
AuthorsLazarus, M.B. / Jiang, J. / Gloster, T.M. / Zandberg, W.F. / Vocadlo, D.J. / Walker, S.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Structural snapshots of the reaction coordinate for O-GlcNAc transferase.
Authors: Lazarus, M.B. / Jiang, J. / Gloster, T.M. / Zandberg, W.F. / Whitworth, G.E. / Vocadlo, D.J. / Walker, S.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)327,86424
Polymers323,8984
Non-polymers3,96620
Water32418
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9666
Polymers80,9751
Non-polymers9925
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)81,9666
Polymers80,9751
Non-polymers9925
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)81,9666
Polymers80,9751
Non-polymers9925
Water0
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)81,9666
Polymers80,9751
Non-polymers9925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules

D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules

D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules

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
hetero molecules

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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)983,59372
Polymers971,69412
Non-polymers11,89960
Water1629
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_564-y,x-y+1,z-11
crystal symmetry operation3_454-x+y-1,-x,z-11
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area48370 Å2
ΔGint-708 kcal/mol
Surface area310280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.039, 272.039, 142.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 / OGT


Mass: 80974.508 Da / Num. of mol.: 4
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, protein O-GlcNAc transferase
#2: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.69 Å3/Da / Density % sol: 73.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.075→49.13 Å / Num. all: 111721 / Num. obs: 111721 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.08→3.24 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.075→48.343 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 5596 5.01 %RANDOM
Rwork0.1996 ---
all0.2011 111695 --
obs0.2011 111695 99.66 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.186 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.08 Å2-0 Å2-0 Å2
2--8.08 Å20 Å2
3----16.16 Å2
Refinement stepCycle: LAST / Resolution: 3.075→48.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22112 0 236 18 22366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322848
X-RAY DIFFRACTIONf_angle_d0.59631016
X-RAY DIFFRACTIONf_dihedral_angle_d11.1468540
X-RAY DIFFRACTIONf_chiral_restr0.0433424
X-RAY DIFFRACTIONf_plane_restr0.0034004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.075-3.10990.36391790.34183454X-RAY DIFFRACTION99
3.1099-3.14650.35721960.3443520X-RAY DIFFRACTION99
3.1465-3.18490.39931930.32533468X-RAY DIFFRACTION99
3.1849-3.22520.34912170.31163507X-RAY DIFFRACTION100
3.2252-3.26760.31381640.29083499X-RAY DIFFRACTION100
3.2676-3.31240.30881850.27683517X-RAY DIFFRACTION100
3.3124-3.35970.28631820.26913554X-RAY DIFFRACTION100
3.3597-3.40980.28961800.24793491X-RAY DIFFRACTION100
3.4098-3.46310.28981670.25333534X-RAY DIFFRACTION100
3.4631-3.51990.26111910.23783510X-RAY DIFFRACTION100
3.5199-3.58050.23871800.22593557X-RAY DIFFRACTION100
3.5805-3.64560.23861710.2213496X-RAY DIFFRACTION99
3.6456-3.71570.22981900.20893520X-RAY DIFFRACTION100
3.7157-3.79150.23171870.20443520X-RAY DIFFRACTION100
3.7915-3.87390.2231970.19183517X-RAY DIFFRACTION100
3.8739-3.9640.20491750.18773501X-RAY DIFFRACTION100
3.964-4.06310.23631700.18833565X-RAY DIFFRACTION100
4.0631-4.17290.22751990.1783505X-RAY DIFFRACTION100
4.1729-4.29560.19281800.17273546X-RAY DIFFRACTION100
4.2956-4.43420.21631870.16793569X-RAY DIFFRACTION100
4.4342-4.59250.18641950.15933519X-RAY DIFFRACTION100
4.5925-4.77630.17322020.15453525X-RAY DIFFRACTION100
4.7763-4.99340.18391570.15243568X-RAY DIFFRACTION100
4.9934-5.25640.18122070.16233552X-RAY DIFFRACTION100
5.2564-5.58530.17971810.17143572X-RAY DIFFRACTION100
5.5853-6.01580.20921920.18153579X-RAY DIFFRACTION100
6.0158-6.61980.23791890.18223575X-RAY DIFFRACTION100
6.6198-7.57450.19191970.16473567X-RAY DIFFRACTION99
7.5745-9.53110.15221660.13833605X-RAY DIFFRACTION99
9.5311-48.3490.23162200.20163687X-RAY DIFFRACTION99
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)
12.13350.06131.20673.83090.89252.1330.1726-1.07660.65960.72050.3021-0.5585-0.15450.8295-0.39741.2667-0.0656-0.17651.1597-0.64921.4971-103.804262.900634.403
20.99370.1196-0.25131.41150.32840.7148-0.1667-0.16990.23180.16320.1517-0.0889-0.09570.14610.01610.95480.0513-0.02390.3322-0.0590.4192-111.162139.388129.8398
31.39240.17830.12412.17380.09610.7438-0.0732-0.10090.09890.44240.10660.013-0.14920.0352-0.01711.06740.18660.07350.31720.02980.4636-138.191540.604541.5129
41.89940.0020.52950.71930.11560.4099-0.0255-0.1182-0.35710.07830.05990.45120.238-0.1709-0.05111.12590.0560.05470.27240.04480.7531-142.4149.381227.9888
50.4707-0.0340.11281.3377-0.27710.3549-0.0706-0.503-0.1360.46590.1180.1806-0.0209-0.01-0.02931.33850.40250.157-0.12750.16010.5417-135.969718.809543.9316
64.73860.96681.22425.5134-0.98456.0780.03080.0261-1.30870.49820.13140.08981.5368-1.7993-0.16511.152-0.3821-0.06830.9870.12130.9379-136.593625.2066.7264
70.70180.0935-0.55420.59460.52751.0567-0.0158-0.0531-0.0205-0.13150.06370.16210.30310.0077-0.03771.02040.0121-0.07820.36780.05460.4969-113.131824.2453-1.2556
81.22970.2567-0.24510.8099-0.19491.03770.0147-0.0664-0.12440.14920.00440.1290.18560.0537-0.01030.7454-0.004-0.04280.23890.01690.4968-118.067824.259-30.3119
91.3880.3688-0.94022.9957-1.73993.0169-0.0219-0.0183-0.23830.1548-0.1686-0.55890.40630.68750.19430.56430.1145-0.0780.59840.00840.5088-83.93126.4418-33.2649
101.48490.1819-0.2631.02510.04680.759-0.0107-0.1888-0.3845-0.0133-0.0059-0.16830.47840.39350.03470.92580.1919-0.04830.36530.0580.5706-98.779313.641-31.5749
117.30821.3208-0.53296.42850.8355.2752-0.65930.804-0.6047-1.85490.7748-1.05040.05591.0623-0.09911.5258-0.14380.3690.9162-0.12350.7903-90.949848.3178-19.0599
121.94960.78990.94081.26380.47251.60840.30760.0918-0.1113-0.3002-0.0242-0.44030.31240.1823-0.2870.8853-0.0260.0340.4443-0.03820.737-87.542646.56075.5743
130.46390.03780.24471.73740.61512.39440.04330.0199-0.0561-0.1527-0.0249-0.4885-0.08440.39560.00240.5179-0.21370.0250.64250.00980.6908-76.654173.494210.6459
141.0109-1.3324-0.59712.85231.571.8071-0.0163-0.3254-0.1780.4620.0826-0.21990.22220.313-0.06810.979-0.2712-0.25350.68370.14030.7388-78.928564.911943.8262
151.2692-0.28980.0230.79710.57242.07250.0616-0.0675-0.10840.33480.0012-0.68950.23780.6027-0.06640.7494-0.1203-0.2160.72020.02681.0328-67.064464.060928.1861
162.89130.4170.10444.2513-0.50351.6315-0.36240.42121.0855-0.0907-0.193-1.4838-0.46890.60420.49521.0626-0.349-0.29220.91780.241.6191-109.33597.979691.1393
171.6513-0.9366-0.95342.55050.98441.8550.098-0.1980.1392-0.1584-0.1729-0.3489-0.44260.27220.07440.5342-0.0905-0.07240.42480.09320.5559-115.972577.150579.715
181.21720.16270.01982.792-0.06791.1499-0.0053-0.00060.38560.062-0.0283-0.2378-0.28870.36040.02090.5321-0.1844-0.05650.42890.01980.4897-96.241458.528691.6256
190.67110.7351-0.17622.6092-1.73981.5874-0.03120.1627-0.2405-0.31730.0297-0.02960.55150.0149-0.00820.7699-0.0085-0.06080.3153-0.03650.4497-113.988234.272475.0582
201.5050.43760.41911.45050.31262.6742-0.06720.35730.0264-0.37090.0535-0.15510.10390.51640.00910.60650.04710.04080.45840.03310.3744-99.120446.901873.0739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 313:349 )A313 - 349
2X-RAY DIFFRACTION2( CHAIN A AND RESID 350:514 )A350 - 514
3X-RAY DIFFRACTION3( CHAIN A AND RESID 515:714 )A515 - 714
4X-RAY DIFFRACTION4( CHAIN A AND RESID 719:875 )A719 - 875
5X-RAY DIFFRACTION5( CHAIN A AND RESID 876:1028 )A876 - 1028
6X-RAY DIFFRACTION6( CHAIN B AND RESID 313:349 )B313 - 349
7X-RAY DIFFRACTION7( CHAIN B AND RESID 350:514 )B350 - 514
8X-RAY DIFFRACTION8( CHAIN B AND RESID 515:714 )B515 - 714
9X-RAY DIFFRACTION9( CHAIN B AND RESID 719:875 )B719 - 875
10X-RAY DIFFRACTION10( CHAIN B AND RESID 876:1028 )B876 - 1028
11X-RAY DIFFRACTION11( CHAIN C AND RESID 313:349 )C313 - 349
12X-RAY DIFFRACTION12( CHAIN C AND RESID 350:514 )C350 - 514
13X-RAY DIFFRACTION13( CHAIN C AND RESID 515:714 )C515 - 714
14X-RAY DIFFRACTION14( CHAIN C AND RESID 719:875 )C719 - 875
15X-RAY DIFFRACTION15( CHAIN C AND RESID 876:1028 )C876 - 1028
16X-RAY DIFFRACTION16( CHAIN D AND RESID 313:349 )D313 - 349
17X-RAY DIFFRACTION17( CHAIN D AND RESID 350:514 )D350 - 514
18X-RAY DIFFRACTION18( CHAIN D AND RESID 515:714 )D515 - 714
19X-RAY DIFFRACTION19( CHAIN D AND RESID 719:875 )D719 - 875
20X-RAY DIFFRACTION20( CHAIN D AND RESID 876:1028 )D876 - 1028

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