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- PDB-7qcc: Williams-Beuren syndrome related methyltransferase WBSCR27 in apo-form -

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Basic information

Entry
Database: PDB / ID: 7qcc
TitleWilliams-Beuren syndrome related methyltransferase WBSCR27 in apo-form
ComponentsMethyltransferase-like 27
KeywordsTRANSFERASE / Williams-Beuren syndrome / SAM-dependent methyltransferase / Rossman fold / Class I methyltransferases
Function / homologyorganonitrogen compound metabolic process / S-adenosylmethionine-dependent methyltransferase activity / Methyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Methyltransferase-like 27
Function and homology information
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsPolshakov, V.I. / Mariasina, S.S. / Chang, C.-F.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-04-00318 Russian Federation
CitationJournal: To Be Published
Title: Williams-Beuren syndrome related methyltransferase WBSCR27: from structure to possible function
Authors: Mariasina, S.S. / Chang, C.-F. / Navalayeu, T. / Chugunova, A. / Efimov, S.V. / Zgoda, V.G. / Suzuki, T. / Ivlev, V. / Dontsova, O.A. / Sergiev, P.V. / Polshakov, V.I.
History
DepositionNov 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase-like 27


Theoretical massNumber of molelcules
Total (without water)25,9881
Polymers25,9881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, The apo-form was obtained by complete refolding of protein-ligand complex. The addition of ligand (SAH or SAM) induced energy release observed in ITC ...Evidence: isothermal titration calorimetry, The apo-form was obtained by complete refolding of protein-ligand complex. The addition of ligand (SAH or SAM) induced energy release observed in ITC experiment. It indicate that we are dealing with apo-from of WBSCR27 protein., native gel electrophoresis, Native gel electrophoresis showed that WBSCR27 in our samples is represented by a monomer., gel filtration, The gel filtration experiment indicated that WBSCR27 in our samples is represented by a monomer., NMR relaxation study, NMR relaxation data showed that WBSCR27 in our samples is represented by a monomer.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16480 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Methyltransferase-like 27 / Williams-Beuren syndrome critical region protein 27 / Williams-Beuren syndrome critical region ...Williams-Beuren syndrome critical region protein 27 / Williams-Beuren syndrome critical region protein 27 isoform alpha / Williams-Beuren syndrome critical region protein 27 isoform beta


Mass: 25988.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mettl27, BC002286, Wbscr27 / Plasmid: pET30aTEV-WBSCR27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BGM4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
124isotropic22D 1H-15N HSQC
133isotropic23D HNCO
143isotropic23D HN(CA)CO
153isotropic23D HN(CO)CA
183isotropic23D HNCA
173isotropic23D CBCA(CO)NH
163isotropic23D HN(CA)CB
193isotropic23D HBHA(CO)NH
1103isotropic23D HNHAHB
1113isotropic23D 1H-15N TOCSY
1124isotropic23D (H)CCH-TOCSY
1133isotropic23D 1H-13C NOESY
1142anisotropic3IPAP
1175isotropic33D 15N-1H NOESY
1161isotropic12D DQF-COSY
1183isotropic23D 15N-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-15N] WBSCR27, 10 mM DTT, 0.2 % w/v sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N-apoWB27_195% H2O/5% D2O
solution20.8 mM [U-15N] WBSCR27, 10 mM DTT, 0.2 % sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 0.225 % v/v phage Pf1 stock solution, 95% H2O/5% D2O15N-apoWB27_RDC95% H2O/5% D2O
solution30.8 mM [U-95% 13C; U-99% 15N] WBSCR27, 10 mM DTT, 0.2 % sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N_13C-apoWB27_h2o95% H2O/5% D2O
solution40.3 mM [99% 13CG]-Thr [99% 13CE]-Met [100% 1HG]-Thr [100% 1HE]-Met [U-100% D] [U-98% 15N] WBSCR27, 5 mM DTT, 0.2 % sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 100% D2O15N_13C-apoWB27_d2o100% D2O
solution50.3 mM [99% 13CG]-Thr [99% 13CE]-Met [100% 1HG]-Thr [100% 1HE]-Met [U-100% D] [U-98% 15N] WBSCR27, 5 mM DTT, 0.2 % sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N_wb27_13CH3-apoWB27-Met-Thr95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMWBSCR27[U-15N]1
10 mMDTTnatural abundance1
0.2 % w/vsodium azidenatural abundance1
50 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.8 mMWBSCR27[U-15N]2
10 mMDTTnatural abundance2
0.2 %sodium azidenatural abundance2
50 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
0.225 % v/vphage Pf1 stock solutionnatural abundance2
0.8 mMWBSCR27[U-95% 13C; U-99% 15N]3
10 mMDTTnatural abundance3
0.2 %sodium azidenatural abundance3
50 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
0.3 mMWBSCR27[99% 13CG]-Thr [99% 13CE]-Met [100% 1HG]-Thr [100% 1HE]-Met [U-100% D] [U-98% 15N]4
5 mMDTTnatural abundance4
0.2 %sodium azidenatural abundance4
50 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
0.3 mMWBSCR27[99% 13CG]-Thr [99% 13CE]-Met [100% 1HG]-Thr [100% 1HE]-Met [U-100% D] [U-98% 15N]5
5 mMDTTnatural abundance5
0.2 %sodium azidenatural abundance5
50 mMsodium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
Sample conditionsIonic strength: 100 mM / Label: condition1 / pH: 7.00 / PH err: 0.05 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Lomonosov MSU
Bruker AVANCEBrukerAVANCE8502Academia Sinica
Bruker AVANCEBrukerAVANCE8003Academia Sinica

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
TopSpinBruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
PINE-SPARKYLee Wchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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