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- PDB-5yjf: Co-crystal structure of Human Nicotinamide N-methyltransferase (N... -

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Basic information

Entry
Database: PDB / ID: 5yjf
TitleCo-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with small molecule analog of Nicotinamide
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT / NA / MNA / T2D
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / NAD biosynthesis via nicotinamide riboside salvage pathway / positive regulation of protein deacetylation / Methylation / Nicotinamide salvaging / : ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / NAD biosynthesis via nicotinamide riboside salvage pathway / positive regulation of protein deacetylation / Methylation / Nicotinamide salvaging / : / 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
6-methoxy-1-methyl-2H-pyridine-3-carboxamide / S-ADENOSYL-L-HOMOCYSTEINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSwaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Hallur, M.S. / Rajagopal, S. / Ruf, S. / Dhakshinamoorthy, S. / Kannt, A. / Gosu, R.
CitationJournal: Sci Rep / Year: 2018
Title: A small molecule inhibitor of Nicotinamide N-methyltransferase for the treatment of metabolic disorders.
Authors: Kannt, A. / Rajagopal, S. / Kadnur, S.V. / Suresh, J. / Bhamidipati, R.K. / Swaminathan, S. / Hallur, M.S. / Kristam, R. / Elvert, R. / Czech, J. / Pfenninger, A. / Rudolph, C. / Schreuder, ...Authors: Kannt, A. / Rajagopal, S. / Kadnur, S.V. / Suresh, J. / Bhamidipati, R.K. / Swaminathan, S. / Hallur, M.S. / Kristam, R. / Elvert, R. / Czech, J. / Pfenninger, A. / Rudolph, C. / Schreuder, H. / Chandrasekar, D.V. / Mane, V.S. / Birudukota, S. / Shaik, S. / Zope, B.R. / Burri, R.R. / Anand, N.N. / Thakur, M.K. / Singh, M. / Parveen, R. / Kandan, S. / Mullangi, R. / Yura, T. / Gosu, R. / Ruf, S. / Dhakshinamoorthy, S.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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
C: Nicotinamide N-methyltransferase
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,62712
Polymers126,4174
Non-polymers2,2108
Water1,27971
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1573
Polymers31,6041
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.323, 132.976, 61.317
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nicotinamide N-methyltransferase


Mass: 31604.184 Da / Num. of mol.: 4 / Mutation: K100A,E101A,E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli (E. coli)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-8WO / 6-methoxy-1-methyl-2H-pyridine-3-carboxamide


Mass: 168.193 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.89 Å3/Da / Density % sol: 34.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2M Sodium chloride, 0.1M BIS-TRIS pH 5.8, 25 %(w/v) PEG 3350

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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 315 / 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: 2.48→47.78 Å / Num. obs: 31948 / % possible obs: 96.4 % / Redundancy: 6.4 % / Net I/σ(I): 5.7
Reflection shellHighest resolution: 2.48 Å / Rmerge(I) obs: 0.885 / Rpim(I) all: 0.411

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ROD

3rod


Resolution: 2.49→47.78 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / SU B: 29.043 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28553 1617 5.1 %RANDOM
Rwork0.22374 ---
obs0.22693 30164 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.075 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å2-0.38 Å2
2--1.45 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.49→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7873 0 152 71 8096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228217
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2942.00511161
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1551019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71824.811318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.984151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271525
X-RAY DIFFRACTIONr_chiral_restr0.0910.21266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026162
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.23936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25587
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2312
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3771.55224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67428213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.02233446
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6714.52946
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: 2.487→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 97 -
Rwork0.306 1968 -
obs--84.22 %
Refinement TLS params.

Method: refined / 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)
11.8216-0.2626-0.061.3182-0.44892.0306-0.00510.10910.0137-0.06810.0344-0.0212-0.0026-0.0644-0.0293-0.10750.00640.0105-0.14640.0136-0.09331.9108-0.39683.7471
22.0640.3874-0.06571.63330.11441.9199-0.0233-0.1335-0.01450.0840.0311-0.0131-0.03350.1014-0.0078-0.0922-0.00670.0156-0.1366-0.0059-0.106425.2687-0.194728.5924
32.3776-0.79650.47572.6317-0.53072.7123-0.1484-0.0080.32820.1637-0.0541-0.0825-0.19380.060.2024-0.0875-0.0095-0.0228-0.07450.01-0.014132.483529.3095-1.2313
42.54270.66360.57922.87680.1912.4958-0.17370.0020.3577-0.148-0.04280.0922-0.1690.00930.2165-0.0756-0.0051-0.017-0.0694-0.0138-0.00578.937729.5898-26.4157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 260
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION2B5 - 260
4X-RAY DIFFRACTION2B301 - 302
5X-RAY DIFFRACTION3C5 - 261
6X-RAY DIFFRACTION3C301 - 302
7X-RAY DIFFRACTION4D5 - 260
8X-RAY DIFFRACTION4D301 - 302

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