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- PDB-9h5o: NNMT-SAM IN COMPLEX WITH 20s -

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Basic information

Entry
Database: PDB / ID: 9h5o
TitleNNMT-SAM IN COMPLEX WITH 20s
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT SAH SAM
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / Methylation / : / positive regulation of gluconeogenesis / methylation / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJohansson, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Mechanism and kinetics of turnover inhibitors of nicotinamide N-methyl transferase in vitro and in vivo.
Authors: Akerud, T. / De Fusco, C. / Brandt, P. / Bergstrom, F. / Johansson, P. / Ek, M. / Borjesson, U. / Johansson, A. / Danielsson, J. / Bauer, M. / Arnaud, B. / Castaldo, M. / Stromstedt, M. / ...Authors: Akerud, T. / De Fusco, C. / Brandt, P. / Bergstrom, F. / Johansson, P. / Ek, M. / Borjesson, U. / Johansson, A. / Danielsson, J. / Bauer, M. / Arnaud, B. / Castaldo, M. / Stromstedt, M. / Rosengren, B. / Jansen, F. / Fredlund, L.
History
DepositionOct 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,7836
Polymers62,6532
Non-polymers1,1294
Water6,233346
1
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8913
Polymers31,3271
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8913
Polymers31,3271
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.28, 69.71, 114.53
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 31326.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical ChemComp-A1IPM / 1,4-dimethyl-6-(methylamino)pyridine-3-carboxamide


Mass: 180.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 32% PEG3350, 0.2 M NaAc, and 0.1 M Hepes pH 6.8-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.63→44.3 Å / Num. obs: 40039 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.99 / Net I/σ(I): 4.7
Reflection shellResolution: 1.63→1.67 Å / Num. unique obs: 818 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.04 Å / Cor.coef. Fo:Fc: 0.726 / Cor.coef. Fo:Fc free: 0.677 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.224 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2022 -RANDOM
Rwork0.254 ---
obs0.255 40039 100 %-
Displacement parametersBiso mean: 12.39 Å2
Baniso -1Baniso -2Baniso -3
1-7.6188 Å20 Å20 Å2
2--9.901 Å20 Å2
3----17.5198 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 78 346 4318
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014085HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975541HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1410SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes705HARMONIC5
X-RAY DIFFRACTIONt_it4085HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion522SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4988SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion16.04
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection% reflection
Rfree0.2738 38 -
Rwork0.2955 --
obs0.2945 801 100 %
Refinement TLS params.

L11: _ / L33: _ / Refine-ID: X-RAY DIFFRACTION

IDL12 (°2)L13 (°2)L22 (°2)L23 (°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)
1-2.24653.3850.6517-2.97150.0394-0.6808-0.2941-0.6808-0.0984-0.4297-0.2941-0.42970.059-0.4398-0.01850.175-0.5031-0.1978-0.34222.5087-24.365772.5708
2-0.4963-5.174102.17450.0914-0.67450.2546-0.6745-0.05080.08710.25460.0871-0.0406-0.5625-0.1506-0.1384-0.5717-0.1683-0.568327.9385-46.959372.4291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|* }
2X-RAY DIFFRACTION2{ D|* }

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