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- PDB-1w3b: The superhelical TPR domain of O-linked GlcNAc transferase reveal... -

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Basic information

Entry
Database: PDB / ID: 1w3b
TitleThe superhelical TPR domain of O-linked GlcNAc transferase reveals structural similarities to importin alpha.
ComponentsUDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110
KeywordsTRANSFERASE / OGT / GLCNAC / NUCLEOPORIN / O-LINKED GLYCOSYLATION / TPR REPEAT / PROTEIN BINDING / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / 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 / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / mitophagy / 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 / positive regulation of translation / cell projection / response to insulin / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / cellular response to glucose stimulus / mitochondrial membrane / protein processing / chromatin DNA binding / Regulation of necroptotic cell death / UCH proteinases / chromatin organization / HATs acetylate histones / positive regulation of cold-induced thermogenesis / apoptotic process / 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 / nucleus / plasma membrane / cytosol
Similarity search - Function
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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 / Mainly Alpha
Similarity search - Domain/homology
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsJinek, M. / Rehwinkel, J. / Lazarus, B.D. / Izaurralde, E. / Hanover, J.A. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The Superhelical Tpr-Repeat Domain of O-Linked Glcnac Transferase Exhibits Structural Similarities to Importin Alpha
Authors: Jinek, M. / Rehwinkel, J. / Lazarus, B.D. / Izaurralde, E. / Hanover, J.A. / Conti, E.
History
DepositionJul 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110
B: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0533
Polymers87,0122
Non-polymers401
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.320, 75.510, 77.670
Angle α, β, γ (deg.)105.08, 105.14, 110.28
Int Tables number1
Space group name H-MP1
DetailsTHE AUTHORS HAVE INDICATED THAT THERE IS EXPERIMENTALEVIDENCE AVAILABLE FROM GEL FILTRATION EXPERIMENTS THATTHIS PROTEIN IS A CONSTITUTIVE DIMER IN SOLUTION, WHICHIS DISCUSSED IN THE JOURNAL REFERENCE ABOVE.

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110 / O-GLCNAC TRANSFERASE P110 SUBUNIT


Mass: 43506.234 Da / Num. of mol.: 2 / Fragment: TPR DOMAIN, RESIDUES 16-400
Source method: isolated from a genetically manipulated source
Details: ISOFORM 2 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-BASED VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O15294, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPRO14 AND MET15 IN BOTH CHAINS A AND B ARE DERIVED FROM THE EXPRESSION PLASMID AND THEREFORE DO NOT ...PRO14 AND MET15 IN BOTH CHAINS A AND B ARE DERIVED FROM THE EXPRESSION PLASMID AND THEREFORE DO NOT CORRESPOND TO THE UNIPROT DATABASE ENTRY O15294

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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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growpH: 7.5 / Details: 0.1M HEPES-NA/HCL PH 7.5 0.2M CACL2 36% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: Nov 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 27841 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.5 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→200 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.2974 1090 3.8 %RANDOM
Rwork0.2594 ---
obs0.2594 27841 97.6 %-
Solvent computationBsol: 67.9029 Å2 / ksol: 0.337687 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.47 Å2-8.855 Å2-4.051 Å2
2---7.991 Å2-15.159 Å2
3---5.521 Å2
Refinement stepCycle: LAST / Resolution: 2.85→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 1 27 5596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007478
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.25408
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM

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