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- PDB-4gz6: Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4gz6
TitleCrystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc
ComponentsUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / OGT / O-GlcNAc / GT-B / Glycosyltransferase / O-GlcNAcylation
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / 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 ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / 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 / 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 / Sin3-type complex / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / histone acetyltransferase complex / mitophagy / 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 / Regulation of necroptotic cell death / chromatin DNA binding / protein processing / UCH proteinases / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / glutamatergic synapse / 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 / 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 / Tetratricopeptide repeat domain / Glycogen Phosphorylase B; ...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 / Tetratricopeptide repeat domain / Glycogen Phosphorylase B; / Tetratricopeptide repeat / 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
Chem-12V / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 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)328,02525
Polymers323,8984
Non-polymers4,12721
Water97354
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9826
Polymers80,9751
Non-polymers1,0085
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)82,0787
Polymers80,9751
Non-polymers1,1046
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)81,9826
Polymers80,9751
Non-polymers1,0085
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)81,9826
Polymers80,9751
Non-polymers1,0085
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)984,07475
Polymers971,69412
Non-polymers12,38063
Water21612
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 area35610 Å2
ΔGint-699 kcal/mol
Surface area314910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.338, 272.338, 143.460
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-12V / (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE


Mass: 623.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O16P2S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 4.74 Å3/Da / Density % sol: 74.06 %
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 Å
DetectorType: DECTRIS 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 Å / Relative weight: 1
ReflectionResolution: 2.98→40 Å / Num. all: 122037 / Num. obs: 122037 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.98→3.14 Å / % possible all: 99

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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: 2.98→39.412 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 6154 5.04 %RANDOM
Rwork0.197 ---
all0.1983 122016 --
obs0.1983 122016 97.99 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.128 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.7676 Å2-0 Å2-0 Å2
2--9.7676 Å20 Å2
3----19.5352 Å2
Refinement stepCycle: LAST / Resolution: 2.98→39.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22112 0 241 54 22407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222852
X-RAY DIFFRACTIONf_angle_d0.5631022
X-RAY DIFFRACTIONf_dihedral_angle_d10.2678520
X-RAY DIFFRACTIONf_chiral_restr0.0413424
X-RAY DIFFRACTIONf_plane_restr0.0034004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.01380.34651970.33413864X-RAY DIFFRACTION99
3.0138-3.04930.33872270.31953879X-RAY DIFFRACTION99
3.0493-3.08650.32082140.31263854X-RAY DIFFRACTION99
3.0865-3.12550.30082060.30573850X-RAY DIFFRACTION99
3.1255-3.16660.31932080.30483895X-RAY DIFFRACTION99
3.1666-3.210.3482330.29353813X-RAY DIFFRACTION99
3.21-3.25580.30122020.28413863X-RAY DIFFRACTION99
3.2558-3.30440.28732040.26393856X-RAY DIFFRACTION99
3.3044-3.3560.27691950.26253871X-RAY DIFFRACTION98
3.356-3.4110.27351970.24123885X-RAY DIFFRACTION99
3.411-3.46980.30411860.23763881X-RAY DIFFRACTION99
3.4698-3.53280.25412000.23783845X-RAY DIFFRACTION98
3.5328-3.60070.24161960.22253845X-RAY DIFFRACTION98
3.6007-3.67420.23591960.21243845X-RAY DIFFRACTION98
3.6742-3.7540.21612050.2043863X-RAY DIFFRACTION98
3.754-3.84130.20822140.193819X-RAY DIFFRACTION98
3.8413-3.93720.20512060.18323860X-RAY DIFFRACTION98
3.9372-4.04360.19611870.17813861X-RAY DIFFRACTION98
4.0436-4.16240.21542210.18043834X-RAY DIFFRACTION98
4.1624-4.29660.18441990.16463884X-RAY DIFFRACTION98
4.2966-4.450.21261960.16383876X-RAY DIFFRACTION98
4.45-4.62790.19242100.15963825X-RAY DIFFRACTION97
4.6279-4.83820.19042160.15353833X-RAY DIFFRACTION98
4.8382-5.09280.17391890.15573861X-RAY DIFFRACTION98
5.0928-5.41110.17372160.16623890X-RAY DIFFRACTION98
5.4111-5.82770.19632070.17063848X-RAY DIFFRACTION97
5.8277-6.41190.2142090.18713872X-RAY DIFFRACTION97
6.4119-7.33450.21552080.17493882X-RAY DIFFRACTION97
7.3345-9.22110.16121920.143879X-RAY DIFFRACTION96
9.2211-39.41560.212180.18573929X-RAY DIFFRACTION95
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)
15.2505-0.9170.68623.80230.98644.45940.3334-1.78331.5360.5615-0.00830.0198-0.03040.4755-0.26911.089-0.25590.0841.0747-0.49161.1305-104.014462.952834.7455
21.51220.4524-0.46661.7305-0.56651.5121-0.1551-0.12390.2669-0.00950.1685-0.0314-0.11610.1117-0.02760.90820.02470.01250.4002-0.07040.5586-111.071739.390630.0862
31.73750.82720.12952.79480.29711.3866-0.0467-0.08750.10620.24260.06040.0348-0.07160.0569-0.0110.88530.1060.04970.29080.00950.4792-138.293340.649741.743
42.1677-0.2960.60030.9880.16430.7188-0.0496-0.0212-0.404-0.0102-0.00280.42860.3385-0.11410.0411.15020.00190.01020.30150.01850.7354-142.20199.16828.2331
50.4387-0.1317-0.06161.7166-0.40850.4489-0.0519-0.2644-0.11570.32840.04170.08890.2090.00290.00341.05490.13430.02540.36460.06080.6098-135.906118.738244.2529
64.15681.49891.38734.7044-0.49356.99860.3401-0.0807-1.11780.39210.144-0.0721.3735-1.7325-0.47491.1899-0.3019-0.09950.92680.120.8918-136.451625.14566.5298
70.99360.2337-0.55410.46040.39141.48640.008-0.0776-0.0927-0.05040.09530.01020.48140.0313-0.09041.02490.0002-0.05330.380.03710.5333-112.793624.2726-1.438
81.72660.2171-0.27220.2296-0.05491.3829-0.008-0.0652-0.12070.2384-0.01270.0560.27260.02290.00740.85940.0056-0.02180.26490.00210.5809-117.881824.4657-30.7037
91.06920.8001-0.832.9417-1.87093.0691-0.0177-0.0691-0.29360.1535-0.0796-0.47610.44750.65450.11340.68450.1482-0.06330.6136-0.00720.6162-83.572626.6246-33.7075
101.44420.3398-0.15570.855200.4819-0.0628-0.0694-0.46860.06440.0272-0.14010.4710.34180.02880.98050.1828-0.03540.42310.02270.6285-98.465613.7894-32.0119
116.23940.669-0.15015.85850.9184.8919-0.28790.6552-0.2096-1.72940.6909-0.95310.62660.7348-0.49191.5688-0.20730.30490.8028-0.17760.837-90.668148.6833-19.1625
121.50160.30471.01240.92380.52242.22530.25760.0836-0.1238-0.27380.0303-0.32930.33960.2198-0.29880.878-0.03010.06380.5655-0.02890.8101-87.19546.80645.6221
130.4910.17780.3251.46990.64523.1996-0.04580.1128-0.1242-0.23550.0869-0.439-0.12880.52-0.01830.5144-0.19270.07550.7039-0.02390.677-76.509873.954310.6204
140.8391-0.9593-0.27642.8271.72822.57-0.0014-0.3139-0.07340.49680.1291-0.39720.250.4428-0.12830.7903-0.1612-0.14960.7720.07720.737-78.631865.129643.9627
151.1741-0.21550.10121.20990.13982.21270.0003-0.0971-0.12850.13210.0252-0.71170.24530.7203-0.02510.5856-0.025-0.11290.7922-0.0110.9537-66.735364.484228.2372
164.0928-0.5211.0216.668-2.2373.576-0.44950.58771.8150.2547-0.4973-2.2215-0.83790.8870.91911.0908-0.3055-0.31620.91480.27441.7017-109.429498.213491.9832
171.3883-0.5648-0.47631.86560.88941.57790.0459-0.1520.1379-0.079-0.1261-0.2178-0.35710.19230.05570.6424-0.1188-0.05790.47310.07560.6187-116.022877.34380.4314
181.35910.18240.17222.989-0.10971.4759-0.00260.01770.30970.1165-0.0261-0.2507-0.34820.36630.01690.5938-0.1871-0.04180.48140.03010.5309-96.080458.840892.4392
190.99850.4277-0.30283.3049-2.13932.34430.0350.1212-0.3295-0.2014-0.00310.0090.60330.0488-0.02770.7282-0.0266-0.02990.3336-0.06240.4883-113.876934.417475.7506
201.70340.51180.89221.07850.52233.0487-0.07590.3129-0.0072-0.2250.0453-0.22270.06370.54170.02390.57640.04090.05660.43530.02510.4748-98.96647.147473.7209
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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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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