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- PDB-5a01: O-GlcNAc transferase from Drososphila melanogaster -

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Basic information

Entry
Database: PDB / ID: 5a01
TitleO-GlcNAc transferase from Drososphila melanogaster
ComponentsO-GLYCOSYLTRANSFERASE
KeywordsTRANSFERASE / O-GLCNAC / PROTEIN POSTTRANSLATIONAL MODIFICATION / TETRATRICOPEPTIDE REPEATS / GLYCOSYLTRANSFERASE / GT41 / N-ACETYLGLUCOSAMINYLTRANSFERASE / EMBRYONIC DEVELOPMENT
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / wing disc development / glycoprotein metabolic process / HATs acetylate histones / UCH proteinases / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of fibroblast growth factor receptor signaling pathway / protein O-linked glycosylation / response to temperature stimulus ...Formation of WDR5-containing histone-modifying complexes / wing disc development / glycoprotein metabolic process / HATs acetylate histones / UCH proteinases / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of fibroblast growth factor receptor signaling pathway / protein O-linked glycosylation / response to temperature stimulus / locomotor rhythm / regulation of gene expression
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 / Tetratricopeptide repeat / TPR repeat / Tetratricopeptide repeat / Glycogen Phosphorylase B; / Tetratricopeptide repeat ...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 / Tetratricopeptide repeat / TPR repeat / Tetratricopeptide repeat / Glycogen Phosphorylase B; / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-12V / protein O-GlcNAc transferase
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsMariappa, D. / Zheng, X. / Schimpl, M. / Raimi, O. / Rafie, K. / Ferenbach, A.T. / Mueller, H.J. / van Aalten, D.M.F.
CitationJournal: Open Biol / Year: 2015
Title: Dual functionality of O-GlcNAc transferase is required for Drosophila development.
Authors: Mariappa, D. / Zheng, X. / Schimpl, M. / Raimi, O. / Ferenbach, A.T. / Muller, H.A. / van Aalten, D.M.
History
DepositionApr 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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 / _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: O-GLYCOSYLTRANSFERASE
B: O-GLYCOSYLTRANSFERASE
C: O-GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,0216
Polymers239,1513
Non-polymers1,8703
Water1,04558
1
A: O-GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3402
Polymers79,7171
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3402
Polymers79,7171
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: O-GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3402
Polymers79,7171
Non-polymers6231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.946, 160.946, 77.189
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A350 - 1060
2111B350 - 1060
3111C350 - 1060

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.492032, 0.870549, -0.007063), (-0.870577, -0.492009, 0.00481), (0.000713, 0.008515, 0.999963)79.70119, 46.54176, -29.50918
3given(-0.57218, -0.820008, -0.01404), (0.819941, -0.572331, 0.011526), (-0.017487, -0.004917, 0.999835)79.89037, -45.77416, 29.70473

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Components

#1: Protein O-GLYCOSYLTRANSFERASE / O-GLCNAC TRANSFERASE


Mass: 79717.078 Da / Num. of mol.: 3
Fragment: CATALYTIC DOMAIN AND 4.5 TPR, UNP RESIDUES 352-1059
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ARCTIC EXPRESS / Variant (production host): RIL
References: UniProt: Q7KJA9, Transferases; Glycosyltransferases, Transferases; Glycosyltransferases; Hexosyltransferases, 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.: 3 / Source method: obtained synthetically / Formula: C17H27N3O16P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACTIVE SITE MUTANT K872M

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: CONDITION 70 OF THE MOLECULAR DIMENSIONS MORPHEUS SCREEN 0.12 M MIX OF D-GLUCOSE, D-MANNOSE, D-GALACTOSE, L-FUCOSE, D-XYLOSE, N-ACETYL-D-GLUCOSAMINE, 30% PEG8000/ETHYLENE GLYCEROL AND 0.1 M TRIS-BICINE PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.886
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.66→35 Å / Num. obs: 63989 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8
Reflection shellResolution: 2.66→2.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PE4

3pe4


Resolution: 2.66→35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.254 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 3238 5.1 %RANDOM
Rwork0.22475 ---
obs0.22672 60715 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.263 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.66→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16026 0 117 58 16201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.96722416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54952028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23924.256726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.048152796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0061590
X-RAY DIFFRACTIONr_chiral_restr0.0850.22562
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112345
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 240 -
Rwork0.39 4342 -
obs--98.58 %

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