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- PDB-3hcb: Crystal Structure of hPNMT in Complex With Noradrenochrome and AdoHcy -

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Basic information

Entry
Database: PDB / ID: 3hcb
TitleCrystal Structure of hPNMT in Complex With Noradrenochrome 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
(3S)-3-hydroxy-2,3-dihydro-1H-indole-5,6-dione / 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. / Gee, C.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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.3Nov 27, 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)64,7916
Polymers63,6922
Non-polymers1,0994
Water4,288238
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3963
Polymers31,8461
Non-polymers5502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3963
Polymers31,8461
Non-polymers5502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-14 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.210, 94.210, 187.900
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: 31845.967 Da / Num. of mol.: 2
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-LT2 / (3S)-3-hydroxy-2,3-dihydro-1H-indole-5,6-dione


Mass: 165.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 62.42 %
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 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 25, 2004
RadiationMonochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→66.5 Å / Num. obs: 33903 / Redundancy: 7.85 % / Biso Wilson estimate: 45.07 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.6
Reflection shellResolution: 2.4→2.43 Å / Redundancy: 7.78 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 4.2

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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→66.5 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.832 / SU ML: 0.36 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3384 9.99 %RANDOM
Rwork0.198 ---
obs0.202 33863 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.115 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 110.12 Å2 / Biso mean: 49 Å2 / Biso min: 23.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 76 238 4431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044308
X-RAY DIFFRACTIONf_angle_d0.9035873
X-RAY DIFFRACTIONf_chiral_restr0.059626
X-RAY DIFFRACTIONf_plane_restr0.007766
X-RAY DIFFRACTIONf_dihedral_angle_d19.1711610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4340.3271490.27712251374100
2.434-2.4710.3561280.26412751403100
2.471-2.5090.2891470.25912271374100
2.509-2.550.2821150.2412721387100
2.55-2.5940.2941200.24112491369100
2.594-2.6420.3031470.24612461393100
2.642-2.6920.31490.24112601409100
2.692-2.7470.2711320.22812221354100
2.747-2.8070.2931610.22712341395100
2.807-2.8720.2941350.23212591394100
2.872-2.9440.2721430.2251254139799
2.944-3.0240.2991380.21212521390100
3.024-3.1130.2661610.21512311392100
3.113-3.2130.2511450.20612451390100
3.213-3.3280.261340.21512881422100
3.328-3.4610.2611390.20512621401100
3.461-3.6190.2221290.18112941423100
3.619-3.810.1981240.1612891413100
3.81-4.0480.1911390.15612791418100
4.048-4.3610.1831400.15312861426100
4.361-4.80.161450.1413011446100
4.8-5.4940.2091660.1612761442100
5.494-6.920.2161500.18813301480100
6.92-66.550.2111480.1851423157199
Refinement TLS params.Method: refined / Origin x: 24.2652 Å / Origin y: 51.2577 Å / Origin z: -5.462 Å
111213212223313233
T0.2372 Å2-0.0301 Å2-0.0241 Å2-0.1551 Å20.0315 Å2--0.0477 Å2
L0.4808 °2-0.1078 °20.0383 °2-0.5236 °2-0.2546 °2---0.0315 °2
S-0.0327 Å °0.0176 Å °0.0416 Å °0.0531 Å °0.0058 Å °0.0097 Å °-0.042 Å °0.0407 Å °0.0252 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 280
2X-RAY DIFFRACTION1allB14 - 281
3X-RAY DIFFRACTION1allA - B2001 - 2002
4X-RAY DIFFRACTION1allA - B3001 - 3002
5X-RAY DIFFRACTION1allB1 - 523
6X-RAY DIFFRACTION1allB235 - 527

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