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- PDB-8or9: Human holo aromatic L-amino acid decarboxylase (AADC) native stru... -

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Basic information

Entry
Database: PDB / ID: 8or9
TitleHuman holo aromatic L-amino acid decarboxylase (AADC) native structure at physiological pH
ComponentsDopa decarboxylase (Aromatic L-amino acid decarboxylase)
KeywordsLYASE / Dopa decarboxilase / Human aromatic amino acid decarboxylase / AADC deficiency / L-dopa / dopamine / pyridoxal phosphate / PLP
Function / homology
Function and homology information


aromatic-L-amino-acid decarboxylase / aromatic-L-amino-acid decarboxylase activity / serotonin biosynthetic process / catecholamine biosynthetic process / carboxylic acid metabolic process / amino acid metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aromatic-L-amino-acid decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aromatic-L-amino-acid decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBisello, G. / Perduca, M. / Bertoldi, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other privateIIS PTCIT100263 Italy
CitationJournal: Protein Sci. / Year: 2023
Title: Human aromatic amino acid decarboxylase is an asymmetric and flexible enzyme: Implication in aromatic amino acid decarboxylase deficiency.
Authors: Bisello, G. / Ribeiro, R.P. / Perduca, M. / Belviso, B.D. / Polverino De' Laureto, P. / Giorgetti, A. / Caliandro, R. / Bertoldi, M.
History
DepositionApr 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dopa decarboxylase (Aromatic L-amino acid decarboxylase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4053
Polymers53,9631
Non-polymers4412
Water4,504250
1
A: Dopa decarboxylase (Aromatic L-amino acid decarboxylase)
hetero molecules

A: Dopa decarboxylase (Aromatic L-amino acid decarboxylase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8096
Polymers107,9262
Non-polymers8834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area13250 Å2
ΔGint-72 kcal/mol
Surface area30310 Å2
Unit cell
Length a, b, c (Å)107.170, 107.170, 218.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-658-

HOH

21A-833-

HOH

31A-842-

HOH

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Components

#1: Protein Dopa decarboxylase (Aromatic L-amino acid decarboxylase) / Dopa decarboxylase (Aromatic L-amino acid decarboxylase) / isoform CRA_a


Mass: 53963.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDC, hCG_1811384, tcag7.584 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53Y41
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes, 40% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→85.45 Å / Num. obs: 59247 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3 / Num. unique obs: 8482

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.13 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 2910 4.92 %
Rwork0.1905 --
obs0.1917 59121 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3667 0 28 250 3945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023783
X-RAY DIFFRACTIONf_angle_d0.5275116
X-RAY DIFFRACTIONf_dihedral_angle_d2.6252256
X-RAY DIFFRACTIONf_chiral_restr0.041556
X-RAY DIFFRACTIONf_plane_restr0.004654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93120.34061480.27782617X-RAY DIFFRACTION100
1.9312-1.96450.28351370.25662622X-RAY DIFFRACTION100
1.9645-2.00020.29661240.25642656X-RAY DIFFRACTION100
2.0002-2.03870.26051350.24972622X-RAY DIFFRACTION100
2.0387-2.08030.26031370.23922623X-RAY DIFFRACTION100
2.0803-2.12550.22641450.22172634X-RAY DIFFRACTION100
2.1255-2.1750.20721390.1972641X-RAY DIFFRACTION100
2.175-2.22940.2411460.2132633X-RAY DIFFRACTION100
2.2294-2.28960.21831150.20032648X-RAY DIFFRACTION100
2.2896-2.3570.23921540.19482635X-RAY DIFFRACTION100
2.357-2.43310.19361360.1822664X-RAY DIFFRACTION100
2.4331-2.52010.20641540.18342601X-RAY DIFFRACTION99
2.5201-2.62090.20241280.17672694X-RAY DIFFRACTION100
2.6209-2.74020.18541400.17792672X-RAY DIFFRACTION100
2.7402-2.88470.22141220.18722684X-RAY DIFFRACTION100
2.8847-3.06540.19861340.18962698X-RAY DIFFRACTION100
3.0654-3.3020.22931420.19562693X-RAY DIFFRACTION100
3.302-3.63420.23191390.18612723X-RAY DIFFRACTION100
3.6342-4.15980.18591350.16872737X-RAY DIFFRACTION99
4.1598-5.23990.1791330.15872783X-RAY DIFFRACTION100
5.2399-48.130.20721670.18142931X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 35.6772 Å / Origin y: -33.4924 Å / Origin z: -9.2458 Å
111213212223313233
T0.1195 Å2-0.0193 Å20.0054 Å2-0.0987 Å20.0205 Å2--0.1181 Å2
L0.3999 °2-0.0409 °2-0.017 °2-0.4375 °2-0.0946 °2--0.5456 °2
S-0.0258 Å °-0.0332 Å °-0.0801 Å °0.0654 Å °-0.0006 Å °-0.0473 Å °0.0732 Å °-0.0158 Å °0.0338 Å °
Refinement TLS groupSelection details: all

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