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- PDB-3hca: Crystal Structure of E185Q hPNMT in Complex With Octopamine and AdoHcy -

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Basic information

Entry
Database: PDB / ID: 3hca
TitleCrystal Structure of E185Q hPNMT in Complex With Octopamine and AdoHcy
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / Catecholamine biosynthesis / Polymorphism / S-adenosyl-L-methionine
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
4-(2R-AMINO-1-HYDROXYETHYL)PHENOL / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsDrinkwater, N. / Martin, J.L.
CitationJournal: Biochem.J. / Year: 2009
Title: Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity.
Authors: Drinkwater, N. / Gee, C.L. / Puri, M. / Criscione, K.R. / McLeish, M.J. / Grunewald, G.L. / Martin, J.L.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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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)64,8277
Polymers63,6902
Non-polymers1,1375
Water5,585310
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4454
Polymers31,8451
Non-polymers6003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3833
Polymers31,8451
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint2 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.180, 94.180, 188.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 31844.982 Da / Num. of mol.: 2 / Mutation: E185Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT, PENT / Plasmid: pET17 PNMT-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


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-OTR / 4-(2R-AMINO-1-HYDROXYETHYL)PHENOL / R-OCTOPAMINE


Mass: 153.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG6K, LiCl, cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 8, 2007 / Details: OSMIC VARI-MAX HF
RadiationMonochromator: OSMIC VARI-MAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→42.11 Å / Num. obs: 30563 / Redundancy: 6.56 % / Biso Wilson estimate: 41.62 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HNN

1hnn


Resolution: 2.4→42.105 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1423 4.96 %RANDOM
Rwork0.193 ---
obs0.195 28699 84.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.319 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 112.18 Å2 / Biso mean: 44.104 Å2 / Biso min: 16.04 Å2
Baniso -1Baniso -2Baniso -3
1-5.433 Å20 Å2-0 Å2
2--5.433 Å2-0 Å2
3----10.866 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 78 310 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044298
X-RAY DIFFRACTIONf_angle_d0.7125849
X-RAY DIFFRACTIONf_chiral_restr0.046621
X-RAY DIFFRACTIONf_plane_restr0.006764
X-RAY DIFFRACTIONf_dihedral_angle_d18.6351600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4860.3531250.311954207963
2.486-2.5850.2981070.2742077218466
2.585-2.7030.3011220.2562226234870
2.703-2.8450.3161290.2472414254376
2.845-3.0240.2691480.2292688283685
3.024-3.2570.2631570.2212908306591
3.257-3.5850.2571590.23101326097
3.585-4.1030.2241460.1613213335998
4.103-5.1680.1661480.1423260340899
5.168-42.1120.1971820.1763435361799
Refinement TLS params.Method: refined / Origin x: 24.103 Å / Origin y: 51.3065 Å / Origin z: -5.7897 Å
111213212223313233
T0.1495 Å2-0.0423 Å2-0.0298 Å2-0.0464 Å20.0389 Å2--0.1384 Å2
L0.2304 °2-0.0806 °20.0607 °2-0.104 °2-0.2509 °2--0.3875 °2
S-0.0529 Å °0.026 Å °0.0908 Å °0.0959 Å °-0.0363 Å °-0.0192 Å °-0.1665 Å °0.0203 Å °0.0735 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 281
2X-RAY DIFFRACTION1allB14 - 281
3X-RAY DIFFRACTION1allA - B3001 - 3002
4X-RAY DIFFRACTION1allA - B401 - 1401
5X-RAY DIFFRACTION1allA1 - 290
6X-RAY DIFFRACTION1allA - B1 - 310

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