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- PDB-4n3a: Crystal Structure of human O-GlcNAc transferase bound to a peptid... -

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Basic information

Entry
Database: PDB / ID: 4n3a
TitleCrystal Structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (1-26)E10A
Components
  • Host cell factor 1
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE/SUBSTRATE / Glycosyltransferase / O-GlcNAc Transferase / Proteolysis Substrate / TPR domain / TPR binding / TRANSFERASE-SUBSTRATE 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 / positive regulation of proteolysis / MLL1 complex / 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 domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Immunoglobulin-like fold / 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 / Host cell factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLazarus, M.B. / Herr, W. / Walker, S.
CitationJournal: Science / Year: 2013
Title: HCF-1 is cleaved in the active site of O-GlcNAc transferase.
Authors: Lazarus, M.B. / Jiang, J. / Kapuria, V. / Bhuiyan, T. / Janetzko, J. / Zandberg, W.F. / Vocadlo, D.J. / Herr, W. / Walker, S.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 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: Host cell factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0153
Polymers83,6112
Non-polymers4041
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-9 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.929, 98.929, 367.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 / Fragment: UNP residues 323-1041
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide Host cell factor 1


Mass: 2636.826 Da / Num. of mol.: 1 / Fragment: HCF-1 pro-repeat2 (UNP residues 1072-1097) / Mutation: E10A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51610
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THIS IS A MUTATION.

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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: 60.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.72M Potassium Phosphate Monobasic, 0.88M Potassium Phosphate Dibasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.88→85.675 Å / Num. all: 82602 / Num. obs: 82602 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.087 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.88-1.983.80.5991.146145120250.59996.1
1.98-2.13.60.3451.940743112740.34595
2.1-2.253.40.2382.435476105730.23894.7
2.25-2.433.20.1882.43143198750.18895.2
2.43-2.663.20.1353.82875689300.13593.4
2.66-2.973.40.1055.82667779250.10591.1
2.97-3.433.40.096.92544674300.0995.5
3.43-4.24.10.0847.42677165170.08498.2
4.2-5.9560.06993081751710.06998.4
5.95-45.8587.90.05312.22285328820.05393.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→45.858 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.852 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 4135 5.01 %Random
Rwork0.2004 ---
obs0.2015 82481 94.31 %-
all-86616 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.6 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 106.9 Å2 / Biso mean: 39.2433 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.1762 Å2-0 Å2-0 Å2
2--0.1762 Å20 Å2
3----0.3524 Å2
Refinement stepCycle: LAST / Resolution: 1.88→45.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5588 0 25 148 5761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075767
X-RAY DIFFRACTIONf_angle_d1.0627835
X-RAY DIFFRACTIONf_chiral_restr0.071872
X-RAY DIFFRACTIONf_plane_restr0.0051016
X-RAY DIFFRACTIONf_dihedral_angle_d132158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.90140.3991410.33512602274395
1.9014-1.92370.32021240.32062605272997
1.9237-1.94720.33191320.28282593272595
1.9472-1.97180.28391570.2642591274897
1.9718-1.99780.26431600.25192568272896
1.9978-2.02520.30271080.2522623273195
2.0252-2.05410.28451340.24542562269695
2.0541-2.08470.26021460.25352572271895
2.0847-2.11730.29421330.23942578271194
2.1173-2.1520.24541490.23332543269293
2.152-2.18910.24881360.21782539267593
2.1891-2.2290.25471290.22232586271595
2.229-2.27180.24471170.21852607272495
2.2718-2.31820.26091340.21522599273394
2.3182-2.36860.24681420.22462589273195
2.3686-2.42370.28181410.21992570271194
2.4237-2.48430.24161550.2242551270693
2.4843-2.55150.26211200.2232540266092
2.5515-2.62650.25591220.21692508263091
2.6265-2.71130.22111280.20582511263991
2.7113-2.80820.23241380.20852486262490
2.8082-2.92060.23031160.2112508262490
2.9206-3.05350.23311510.20342533268492
3.0535-3.21450.20111340.20652639277394
3.2145-3.41580.21081290.19082734286397
3.4158-3.67940.23131480.18272745289398
3.6794-4.04950.19111520.16422746289897
4.0495-4.6350.1681480.15032793294197
4.635-5.83770.17121750.16572819299498
5.8377-45.87170.19981360.19972906304292
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)
13.9705-0.40080.20762.15850.59863.6710.0465-0.16970.2714-0.03020.05630.0644-0.4179-0.3287-0.07440.31150.14990.0690.4395-0.09270.3309-16.2921-38.319856.6552
21.74130.028-0.25591.1335-0.20551.3386-0.1062-0.41970.20640.18860.13180.0043-0.1-0.0438-0.03790.23020.06150.02380.3796-0.04840.2381-6.9874-46.483155.3624
31.50020.10850.48131.42290.07192.56640.05170.1129-0.03510.05350.0873-0.06880.1243-0.2913-0.08230.1852-0.0129-0.01570.23370.01430.1634-8.9163-55.233641.9158
40.2129-0.0398-0.27741.3001-0.24172.39690.0011-0.170.079-0.0140.06450.04030.0938-0.3853-0.04730.16830.01790.00310.4440.04470.2448-18.4982-51.488826.6612
52.21680.62560.18852.39450.12771.67340.1201-0.45440.2640.2336-0.02180.143-0.2492-0.1959-0.03180.27520.10330.05280.4745-0.01050.3164-19.3577-35.75428.8413
60.845-0.37550.01260.85360.48031.94680.0333-0.25420.30160.23680.0723-0.1843-0.33140.3959-0.05540.3581-0.1132-0.02950.4143-0.12120.42358.7467-28.419429.7861
70.6651-0.073-0.33661.22180.12441.70230.08670.02710.37750.07730.04030.0613-0.4727-0.1249-0.06840.26050.01640.02240.2531-0.01120.3972-2.5743-26.208616.5351
82.111-0.5963-1.64222.1567-0.42891.83070.03960.36660.2188-0.5815-0.3628-0.12550.05840.51860.20830.24-0.02120.06630.6320.11740.260111.6869-46.6597-11.6838
92.85130.3115-0.47060.875-0.89213.72520.14360.7321-0.0365-0.4394-0.17880.15430.1465-0.12870.11770.3224-0.03290.08050.493-0.05460.299511.167-52.1631-12.4416
101.5619-0.1154-0.5540.5261-0.08321.1196-0.10630.1122-0.0683-0.06750.0429-0.0840.0160.06550.02560.1565-0.03850.0030.29470.01030.21944.8376-50.27092.6784
111.601-0.4335-0.03331.2301-0.91461.0419-0.06560.3326-0.1159-0.170.14190.16450.1957-0.3004-0.03540.1588-0.0462-0.03980.35590.04520.2121-13.2896-50.04213.1816
121.3704-0.2854-0.28140.6634-0.05831.8333-0.00460.24940.2282-0.09270.07470.0267-0.1614-0.2681-0.03740.1484-0.0056-0.00480.2910.07740.24-6.0808-38.19331.9926
131.4837-0.49690.37911.50490.9681.0077-0.09970.56561.013-0.0022-0.24120.0171-1.4990.21410.17120.9004-0.1505-0.01330.1887-0.05610.78212.5791-13.147321.7367
141.7955-0.3207-1.64783.0205-0.16269.4910.0699-0.08560.20420.25550.0478-0.02980.05920.04310.00990.24640.05080.05360.46720.11170.3074-14.3927-47.210844.5632
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
14X-RAY DIFFRACTION14(CHAIN B AND RESID 13:24)B13 - 24

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