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- PDB-7twu: Crystal structure of human phenylethanolamine N-methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 7twu
TitleCrystal structure of human phenylethanolamine N-methyltransferase (PNMT) in complex with (2S)-2-amino-4-(((5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(4-(7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl)butyl)amino)butanoic acid and AdoHcy (SAH)
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / Transition state analogue / Chemical synthesis / Drug design / neurodegenerative disease / PNMT
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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / Chem-KNX / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHarijan, R.K. / Mahmoodi, N. / Minnow, Y.V.T. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2023
Title: Cell-Effective Transition-State Analogue of Phenylethanolamine N -Methyltransferase.
Authors: Mahmoodi, N. / Minnow, Y.V.T. / Harijan, R.K. / Bedard, G.T. / Schramm, V.L.
History
DepositionFeb 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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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)66,70720
Polymers64,6552
Non-polymers2,05118
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.754, 93.754, 188.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32327.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT, PENT / Production host: Escherichia coli (E. coli)
References: UniProt: P11086, phenylethanolamine N-methyltransferase

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Non-polymers , 5 types, 138 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-KNX / 5'-([(3S)-3-amino-3-carboxypropyl]{4-[(4R)-7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl]butyl}amino)-5'-deoxyadenosine


Mass: 623.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36Cl2N8O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium cacodylate pH 5.5, 170 mM LiCl, 18 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→93.75 Å / Num. obs: 49863 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3995 / CC1/2: 0.83 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MIK

4mik


Resolution: 2.1→38.369 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 2474 4.98 %
Rwork0.2009 47242 -
obs0.2026 49716 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.75 Å2 / Biso mean: 61.4207 Å2 / Biso min: 38.21 Å2
Refinement stepCycle: final / Resolution: 2.1→38.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 129 120 4353
Biso mean--66.93 60.3 -
Num. residues----526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.14040.34211250.30342602
2.1404-2.18410.33591100.30932592
2.1841-2.23160.32681460.28392560
2.2316-2.28350.31741350.26642572
2.2835-2.34060.29651490.26662556
2.3406-2.40390.30441480.2592588
2.4039-2.47460.31141450.25152579
2.4746-2.55440.3221370.24932588
2.5544-2.64570.31691520.25312583
2.6457-2.75160.26421460.24912580
2.7516-2.87680.26651290.23842627
2.8768-3.02840.29741300.24532633
3.0284-3.21810.26931330.23922623
3.2181-3.46640.27721320.22562635
3.4664-3.8150.21961190.19382671
3.815-4.36630.22581560.17512653
4.3663-5.49850.17051370.15772732
5.4985-38.3690.18191450.16432868

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