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- PDB-3rch: Crystal structure of Human aromatic L-amino acid decarboxylase (A... -

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Basic information

Entry
Database: PDB / ID: 3rch
TitleCrystal structure of Human aromatic L-amino acid decarboxylase (AADC) in the open conformation with LLP and PLP bound to Chain-A and Chain-B respectively
Components(aromatic L-amino acid decarboxylase) x 2
KeywordsLYASE / apo enzyme / apo form / open conformation / open dimer / exposed / conformational change / Parkinson / AADC deficiency / DDC / LLP / PLP / decarboxylase / L-DOPA / internal aldimine / Shiff Base
Function / homology
Function and homology information


L-dopa decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / aromatic-L-amino-acid decarboxylase activity / Serotonin and melatonin biosynthesis / serotonin biosynthetic process / Catecholamine biosynthesis / catecholamine metabolic process / carboxylic acid metabolic process / amino acid metabolic process ...L-dopa decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / aromatic-L-amino-acid decarboxylase activity / Serotonin and melatonin biosynthesis / serotonin biosynthetic process / Catecholamine biosynthesis / catecholamine metabolic process / carboxylic acid metabolic process / amino acid metabolic process / dopamine biosynthetic process / kidney development / response to toxic substance / pyridoxal phosphate binding / gene expression / enzyme binding / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
dopa decarboxylase, N-terminal domain / dopa decarboxylase, N-terminal domain / 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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 ...dopa decarboxylase, N-terminal domain / dopa decarboxylase, N-terminal domain / 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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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 / molecular replacement / Resolution: 2.8 Å
AuthorsGiardina, G. / Montioli, R. / Gianni, S. / Cellini, B. / Paiardini, A. / Borri Voltattorni, C. / Cutruzzola, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases.
Authors: Giardina, G. / Montioli, R. / Gianni, S. / Cellini, B. / Paiardini, A. / Voltattorni, C.B. / Cutruzzola, F.
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aromatic L-amino acid decarboxylase
B: aromatic L-amino acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4023
Polymers108,1552
Non-polymers2471
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-60 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.000, 177.000, 74.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

#1: Protein aromatic L-amino acid decarboxylase / AADC / DOPA decarboxylase / DDC


Mass: 54191.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Monomer-A with PLP bound and internal aldimine formed (K303+PLP = LLP)
Source: (gene. exp.) Homo sapiens (human) / Gene: AADC / Plasmid: pTrcHis2A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P20711, aromatic-L-amino-acid decarboxylase
#2: Protein aromatic L-amino acid decarboxylase / AADC / DOPA decarboxylase / DDC


Mass: 53963.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Monomer-A with PLP bound and internal aldimine formed (K303+PLP = LLP)
Source: (gene. exp.) Homo sapiens (human) / Gene: AADC / Plasmid: pTrcHis2A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P20711, aromatic-L-amino-acid decarboxylase
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, soaking / pH: 7
Details: crystals obtained from holoAADC in 0.1 M HEPES pH 7.0, 28-30% Jeffamine ED 2001 pH 7.0 were transferred in a ML droplet containing 10mM PLP to yield crystals with PLP and LLP bound, vapor ...Details: crystals obtained from holoAADC in 0.1 M HEPES pH 7.0, 28-30% Jeffamine ED 2001 pH 7.0 were transferred in a ML droplet containing 10mM PLP to yield crystals with PLP and LLP bound, vapor diffusion, soaking, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
51
61
71
81
91
101
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→125.158 Å / Num. all: 29907 / Num. obs: 29907 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.133 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueDiffraction-ID% possible all
2.8-2.957.20.6121.23083342850.6121100
2.95-3.137.20.4151.82928540620.4152100
3.13-3.357.20.2942.62734038150.2943100
3.35-3.617.10.183.52565335880.184100
3.61-3.967.10.1215.92352333010.1215100
3.96-4.437.10.08982133230150.0896100
4.43-5.1170.0739.11872726640.0737100
5.11-6.266.90.088.31587122930.088100
6.26-8.856.70.05212.51210618060.0529100
8.85-49.09160.04213.8649410780.0421099.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RBF

3rbf


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2372 / WRfactor Rwork: 0.1819 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8295 / SU B: 28.045 / SU ML: 0.301 / SU R Cruickshank DPI: 3.2827 / SU Rfree: 0.3682 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1513 5.1 %RANDOM
Rwork0.2005 ---
all0.266 29867 --
obs0.2034 29803 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.11 Å2 / Biso mean: 56.159 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6966 0 16 28 7010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227159
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9599687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88723.365318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.483151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4521550
X-RAY DIFFRACTIONr_chiral_restr0.1020.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215403
X-RAY DIFFRACTIONr_mcbond_it0.631.54420
X-RAY DIFFRACTIONr_mcangle_it1.22727088
X-RAY DIFFRACTIONr_scbond_it1.7832739
X-RAY DIFFRACTIONr_scangle_it3.0494.52596
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 114 -
Rwork0.288 2059 -
all-2173 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.99830.63462.34541.6636-0.36344.0448-0.1891-0.00570.14440.1719-0.1004-0.0739-0.46670.31650.28940.0673-0.0517-0.02440.1430.02750.094167.163737.061-7.968
22.8518-0.3519-0.78660.608-0.11381.5943-0.0150.0325-0.3138-0.09740.02020.04550.3327-0.1713-0.00520.0907-0.0299-0.02810.0295-0.00230.0550.267617.757822.0047
35.0386-2.7781-0.66293.7918-1.0093.8905-0.0246-0.00090.59190.1440.1155-0.1371-0.5675-0.1746-0.09090.09460.0329-0.03170.0903-0.04590.184758.889848.978322.4438
41.1405-0.98610.57460.9901-1.33445.56670.08960.08080.0205-0.2064-0.0961-0.03190.96870.45320.00660.18060.1217-0.02010.2031-0.07080.08474.126211.42181.2869
53.47810.0511-0.87950.08370.03870.8332-0.0439-0.07530.13160.11620.00460.0071-0.0121-0.08830.03930.20160.02450.03640.03840.00620.111538.547121.3156-16.0675
63.02280.0175-0.22015.7051-0.52082.81750.0913-0.4037-0.29910.7907-0.01140.07630.66090.1515-0.07990.3890.0489-0.04570.07760.01520.060955.7295-4.7444-20.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION2A86 - 355
3X-RAY DIFFRACTION3A386 - 480
4X-RAY DIFFRACTION4B1 - 75
5X-RAY DIFFRACTION5B86 - 322
6X-RAY DIFFRACTION6B386 - 480

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