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- PDB-2toh: TYROSINE HYDROXYLASE CATALYTIC AND TETRAMERIZATION DOMAINS FROM RAT -

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Basic information

Entry
Database: PDB / ID: 2toh
TitleTYROSINE HYDROXYLASE CATALYTIC AND TETRAMERIZATION DOMAINS FROM RAT
ComponentsTYROSINE 3-MONOOXYGENASE
KeywordsHYDROXYLASE / NEUROTRANSMITTER BIOSYNTHESIS / NON-HEME IRON / PTERIN CO-SUBSTRATE / CATECHOLAMINE BIOSYNTHESIS / OXIDOREDUCTASE
Function / homology
Function and homology information


Catecholamine biosynthesis / phthalate metabolic process / tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / dopamine biosynthetic process from tyrosine / embryonic camera-type eye morphogenesis / circadian sleep/wake cycle / norepinephrine biosynthetic process / epinephrine biosynthetic process / serotonin biosynthetic process ...Catecholamine biosynthesis / phthalate metabolic process / tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / dopamine biosynthetic process from tyrosine / embryonic camera-type eye morphogenesis / circadian sleep/wake cycle / norepinephrine biosynthetic process / epinephrine biosynthetic process / serotonin biosynthetic process / response to pyrethroid / aminergic neurotransmitter loading into synaptic vesicle / catecholamine biosynthetic process / response to curcumin / hyaloid vascular plexus regression / eye photoreceptor cell development / dopamine binding / response to ether / sphingolipid metabolic process / melanosome membrane / response to growth factor / tetrahydrobiopterin binding / response to insecticide / cellular response to alkaloid / response to steroid hormone / response to herbicide / mating behavior / regulation of heart contraction / response to zinc ion / response to metal ion / amino acid binding / dopamine biosynthetic process / eating behavior / response to corticosterone / small molecule binding / response to immobilization stress / response to isolation stress / neuron projection terminus / smooth endoplasmic reticulum / social behavior / synaptic transmission, dopaminergic / response to electrical stimulus / response to salt stress / response to light stimulus / visual perception / cellular response to manganese ion / response to amphetamine / animal organ morphogenesis / fatty acid metabolic process / ferric iron binding / learning / locomotory behavior / cytoplasmic vesicle membrane / response to activity / cellular response to xenobiotic stimulus / response to nicotine / cellular response to glucose stimulus / monooxygenase activity / memory / cerebral cortex development / oxygen binding / ferrous iron binding / response to nutrient levels / cellular response to growth factor stimulus / cellular response to nicotine / cognition / response to peptide hormone / heart development / cytoplasmic side of plasma membrane / terminal bouton / response to estradiol / synaptic vesicle / response to lipopolysaccharide / cytoplasmic vesicle / response to hypoxia / response to ethanol / perikaryon / neuron projection / response to xenobiotic stimulus / protein domain specific binding / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / enzyme binding / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tyrosine 3-monooxygenase / Tyrosine hydroxylase, conserved site / Tyrosine 3-monooxygenase, catalytic domain / : / Tyrosine hydroxylase N terminal / Tyrosine 3-monooxygenase-like, ACT domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase, iron/copper binding site ...Tyrosine 3-monooxygenase / Tyrosine hydroxylase, conserved site / Tyrosine 3-monooxygenase, catalytic domain / : / Tyrosine hydroxylase N terminal / Tyrosine 3-monooxygenase-like, ACT domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase / Biopterin-dependent aromatic amino acid hydroxylase family profile. / ACT-like domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 7,8-DIHYDROBIOPTERIN / Tyrosine 3-monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGoodwill, K.E. / Sabatier, C. / Stevens, R.C.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of tyrosine hydroxylase with bound cofactor analogue and iron at 2.3 A resolution: self-hydroxylation of Phe300 and the pterin-binding site.
Authors: Goodwill, K.E. / Sabatier, C. / Stevens, R.C.
History
DepositionAug 26, 1998Processing site: BNL
Revision 1.0Aug 26, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6214
Polymers39,2901
Non-polymers3313
Water3,099172
1
A: TYROSINE 3-MONOOXYGENASE
hetero molecules

A: TYROSINE 3-MONOOXYGENASE
hetero molecules

A: TYROSINE 3-MONOOXYGENASE
hetero molecules

A: TYROSINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,48216
Polymers157,1604
Non-polymers1,32212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x,-y+1/2,-z+3/21
crystal symmetry operation11_556-x+1/2,y,-z+3/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area13680 Å2
ΔGint-151 kcal/mol
Surface area55350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)189.464, 148.595, 56.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein TYROSINE 3-MONOOXYGENASE / TYROH


Mass: 39290.090 Da / Num. of mol.: 1
Fragment: CATALYTIC AND TETRAMERIZATION DOMAINS, RESIDUES 160 - 498
Source method: isolated from a genetically manipulated source
Details: IRON AND 7,8-DIHYDROBIOPTERIN AT THE ACTIVE SITE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: BL21 (DE3) PLYSS / Description: FIRST 155 RESIDUES TRUNCATED / Organ: ADRENAL GLAND / Plasmid: PETOHD155 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P04177, tyrosine 3-monooxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.55 Å3/Da / Density % sol: 46 % / Description: RIGID BODY REFINEMENT FROM STARTING MODEL
Crystal growpH: 7.9 / Details: pH 7.9
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein11
21.15 Mammonium sulfate12
33.2 %PEG20012
45 %glycerol12
5100 mMTris12
63 mM7,8-dihydrobiopterin12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 17449 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.31 / % possible all: 81.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1-H

Resolution: 2.3→40 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 2172170.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1171 6.8 %RANDOM
Rwork0.207 ---
obs0.207 17098 94.1 %-
Solvent computationSolvent model: CNS
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å20 Å20 Å2
2--12.83 Å20 Å2
3----17.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 19 172 2907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.29
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.671.5
X-RAY DIFFRACTIONc_mcangle_it4.072
X-RAY DIFFRACTIONc_scbond_it4.232
X-RAY DIFFRACTIONc_scangle_it5.672.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 175 6.8 %
Rwork0.321 2391 -
obs--86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DIHYPTER.PARDIHYPTER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.29

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