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- PDB-9gvw: NNMT-SAH IN COMPLEX WITH 4 -

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Basic information

Entry
Database: PDB / ID: 9gvw
TitleNNMT-SAH IN COMPLEX WITH 4
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT / SAM / SAH
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: 1.241 Å
AuthorsJohansson, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Not funded Sweden
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
DepositionSep 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)63,5226
Polymers62,4792
Non-polymers1,0434
Water8,359464
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7613
Polymers31,2401
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7613
Polymers31,2401
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.887, 69.818, 116.789
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: 31239.545 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-A1IPO / 4-methoxy-2,3-dimethyl-pyridine


Mass: 137.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO / 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.: 464 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.24→46.3 Å / Num. obs: 112304 / % possible obs: 78.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.3
Reflection shellResolution: 1.24→1.28 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 2000

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.241→46.31 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.058 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.06 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.057
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 5598 -RANDOM
Rwork0.1965 ---
obs0.1973 112304 78.4 %-
Displacement parametersBiso mean: 25.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.026 Å20 Å20 Å2
2--3.9056 Å20 Å2
3----4.9316 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.241→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 72 464 4502
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0124154HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185632HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1434SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes698HARMONIC5
X-RAY DIFFRACTIONt_it4154HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion530SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4216SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.82
X-RAY DIFFRACTIONt_other_torsion15.39
LS refinement shellResolution: 1.241→1.29 Å
RfactorNum. reflection% reflection
Rfree0.3567 121 -
Rwork0.3762 --
obs--14.93 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°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)
10.7280.66540.01381.9854-0.12060.34540.08510.13630.04030.1363-0.0859-0.00920.0403-0.00920.0007-0.0282-0.0133-0.0036-0.0227-0.01380.01632.845424.700742.5811
20.59490.1410.23260.9032-0.09260.76650.0490.0454-0.01860.0454-0.00850.015-0.01860.015-0.0405-0.0406-0.00540.0136-0.0207-0.00250.010527.533647.527142.7173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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