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- PDB-2iip: Human Nicotinamide N-methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2iip
TitleHuman Nicotinamide N-methyltransferase
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / mutation / surface mutagenesis / mutant / methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration / positive regulation of gluconeogenesis / response to organonitrogen compound / 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
S-ADENOSYL-L-HOMOCYSTEINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBernstein, G. / Min, J. / Wu, H. / Tempel, W. / Zeng, H. / Loppnau, P. / Avvakumov, G.V. / Wasney, G. / Weigelt, J. / Sundstrom, M. ...Bernstein, G. / Min, J. / Wu, H. / Tempel, W. / Zeng, H. / Loppnau, P. / Avvakumov, G.V. / Wasney, G. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human Nicotinamide N-methyltransferase in complex with SAH
Authors: Bernstein, G. / Min, J. / Wu, H. / Tempel, W. / Zeng, H. / Loppnau, P. / Avvakumov, G.V. / Wasney, G. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999The residue Met -18 is a cloning artifact and also an initiating methionine

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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)127,4028
Polymers125,8644
Non-polymers1,5384
Water5,134285
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8502
Polymers31,4661
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8502
Polymers31,4661
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8502
Polymers31,4661
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8502
Polymers31,4661
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.016, 62.007, 107.073
Angle α, β, γ (deg.)82.35, 81.89, 68.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nicotinamide N-methyltransferase /


Mass: 31466.033 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 / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 20, 2006
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→29.5 Å / Num. all: 64271 / Num. obs: 64271 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 7.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.4 / Num. unique all: 6482 / Rsym value: 0.578 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→29.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.488 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.24 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26477 2208 3.3 %RANDOM
Rwork0.2174 ---
all0.219 64271 --
obs0.21903 64271 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.364 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å2-0.06 Å2
2---0.14 Å2-0.02 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 104 285 8481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228384
X-RAY DIFFRACTIONr_angle_refined_deg1.7852.00111376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80851033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28224.911336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.739151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3761529
X-RAY DIFFRACTIONr_chiral_restr0.1140.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026207
X-RAY DIFFRACTIONr_nbd_refined0.2250.24308
X-RAY DIFFRACTIONr_nbtor_refined0.310.25699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2472
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.214
X-RAY DIFFRACTIONr_mcbond_it0.9851.55318
X-RAY DIFFRACTIONr_mcangle_it1.59228352
X-RAY DIFFRACTIONr_scbond_it2.75133539
X-RAY DIFFRACTIONr_scangle_it4.1264.53024
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.277 4779 -
Rfree-0 -
obs--95.5 %

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