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- PDB-5xvk: Crystal structure of mouse Nicotinamide N-methyltransferase (NNMT... -

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Basic information

Entry
Database: PDB / ID: 5xvk
TitleCrystal structure of mouse Nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl Nicotinamide (MNA)
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT / MNA / ternary complex / feedback inhibition / T2D
Function / homology
Function and homology information


Methylation / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Nicotinamide salvaging / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation ...Methylation / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Nicotinamide salvaging / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation / response to xenobiotic stimulus / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-carbamoyl-1-methylpyridin-1-ium / S-ADENOSYL-L-HOMOCYSTEINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSwaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Kannt, A. / Gosu, R.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structures of monkey and mouse nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl nicotinamide
Authors: Swaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Juluri, S. / Shaik, S. / Anand, N.N. / Burri, R.R. / Kristam, R. / Hallur, M.S. / Rajagopal, S. / Schreuder, H. / ...Authors: Swaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Juluri, S. / Shaik, S. / Anand, N.N. / Burri, R.R. / Kristam, R. / Hallur, M.S. / Rajagopal, S. / Schreuder, H. / Langer, T. / Rudolph, C. / Ruf, S. / Dhakshinamoorthy, S. / Gosu, R. / Kannt, A.
History
DepositionJun 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 14, 2018Group: Non-polymer description / Structure summary / Category: entity
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description
Revision 2.1Dec 4, 2019Group: Data collection / Category: reflns_shell
Revision 2.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7357
Polymers63,6002
Non-polymers1,1355
Water6,035335
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4144
Polymers31,8001
Non-polymers6143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3223
Polymers31,8001
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.138, 71.699, 157.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 31800.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nnmt / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O55239, nicotinamide N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-8GC / 3-carbamoyl-1-methylpyridin-1-ium / 1-methylnicotinamide


Mass: 137.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N2O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.27 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.25M Sodium thiocyanate, 22%(w/v) PEG 3350, 3% TMAO as additive

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.88→78.57 Å / Num. obs: 44282 / % possible obs: 99.7 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.035 / Rrim(I) all: 0.107 / Net I/σ(I): 15.2
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.536 / CC1/2: 0.869 / Rpim(I) all: 0.195 / Rrim(I) all: 0.572 / % possible all: 95.8

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREP8.2.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I62

2i62


Resolution: 1.88→78.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.937 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 2233 5.1 %RANDOM
Rwork0.1843 ---
obs0.1858 41977 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 53.06 Å2 / Biso mean: 15.41 Å2 / Biso min: 5.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.88→78.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 92 335 4507
Biso mean--12.61 25.16 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224312
X-RAY DIFFRACTIONr_angle_refined_deg1.162.0055860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84624.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37915737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7311521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023313
X-RAY DIFFRACTIONr_nbd_refined0.1880.21998
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2312
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.234
LS refinement shellResolution: 1.878→1.927 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 161 -
Rwork0.238 2918 -
all-3079 -
obs--96.19 %

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