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- PDB-2an3: Structure of PNMT with S-adenosyl-L-homocysteine and the semi-rig... -

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Basic information

Entry
Database: PDB / ID: 2an3
TitleStructure of PNMT with S-adenosyl-L-homocysteine and the semi-rigid analogue acceptor substrate cis-(1R,2S)-2-amino-1-tetralol.
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / substrate structure / S-adenosyl-L-methionine / adrenaline synthesis
Function / homology
Function and homology information


phenylethanolamine N-methyltransferase / phenylethanolamine N-methyltransferase activity / epinephrine biosynthetic process / Catecholamine biosynthesis / catecholamine biosynthetic process / 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. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CTL / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsGee, C.L. / Tyndall, J.D.A. / Grunewald, G.L. / Wu, Q. / McLeish, M.J. / Martin, J.L.
CitationJournal: Biochemistry / Year: 2005
Title: Mode of binding of methyl acceptor substrates to the adrenaline-synthesizing enzyme phenylethanolamine N-methyltransferase: implications for catalysis
Authors: Gee, C.L. / Tyndall, J.D.A. / Grunewald, G.L. / Wu, Q. / McLeish, M.J. / Martin, J.L.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,7876
Polymers63,6922
Non-polymers1,0954
Water4,558253
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3943
Polymers31,8461
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3943
Polymers31,8461
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint6 kcal/mol
Surface area20130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.780, 93.780, 187.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-1233-

HOH

Detailsenzyme is active as a monomer

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Components

#1: Protein Phenylethanolamine N-methyltransferase / / PNMTase / Noradrenaline N-methyltransferase


Mass: 31845.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT / Plasmid: pET17PNMT-his / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P11086, phenylethanolamine 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.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CTL / CIS-(1R,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL / CIS-(1R,2S)-1-HYDROXY-2-AMINO-1,2,3,4 TETRAHYDRONAPHTHALENE / CIS-(1R,2S)-2-AMINO-1-TETRALOL


Mass: 163.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 6000, LiCl, cacodylate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2004 / Details: Osmic mirrors (Maxscreen)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→66.31 Å / Num. all: 43227 / Num. obs: 42859 / % possible obs: 99.2 % / Redundancy: 6.67 % / Rmerge(I) obs: 0.079 / Χ2: 0.98 / Net I/σ(I): 12.8 / Scaling rejects: 2162
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 99.4 % / Redundancy: 6.28 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.7 / Num. measured obs: 68 / Num. unique all: 4230 / Χ2: 1.18 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata processing
CNSrefinement
PDB_EXTRACT1.7data extraction
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1HNN

1hnn


Resolution: 2.2→66.31 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4317 10.1 %RANDOM
Rwork0.217 ---
all-43227 --
obs-42856 99.1 %-
Solvent computationBsol: 50.5 Å2
Displacement parametersBiso mean: 44.365 Å2
Baniso -1Baniso -2Baniso -3
1--6.461 Å20 Å20 Å2
2---6.461 Å20 Å2
3---12.923 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.2→66.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 76 253 4440
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.392 419 9.9 %
Rwork0.37 3811 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3sah_mod2.param
X-RAY DIFFRACTION4254_noH.param

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