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- PDB-1toh: TYROSINE HYDROXYLASE CATALYTIC AND TETRAMERIZATION DOMAINS FROM RAT -

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Basic information

Entry
Database: PDB / ID: 1toh
TitleTYROSINE HYDROXYLASE CATALYTIC AND TETRAMERIZATION DOMAINS FROM RAT
ComponentsTYROSINE HYDROXYLASE
KeywordsHYDROXYLASE / NEUROTRANSMITTER BIOSYNTHESIS / NON-HEME IRON / PTERIN CO-SUBSTRATE
Function / homology
Function and homology information


phytoalexin metabolic process / Catecholamine biosynthesis / phthalate metabolic process / glycoside metabolic process / isoquinoline alkaloid metabolic process / terpene metabolic process / tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / dopamine biosynthetic process from tyrosine / circadian sleep/wake cycle ...phytoalexin metabolic process / Catecholamine biosynthesis / phthalate metabolic process / glycoside metabolic process / isoquinoline alkaloid metabolic process / terpene metabolic process / tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / dopamine biosynthetic process from tyrosine / circadian sleep/wake cycle / embryonic camera-type eye morphogenesis / epinephrine biosynthetic process / response to pyrethroid / norepinephrine biosynthetic process / hyaloid vascular plexus regression / catecholamine biosynthetic process / response to curcumin / aminergic neurotransmitter loading into synaptic vesicle / dopamine binding / eye photoreceptor cell development / sphingolipid metabolic process / response to ether / response to growth factor / melanosome membrane / synaptic transmission, dopaminergic / response to insecticide / tetrahydrobiopterin binding / response to steroid hormone / response to metal ion / mating behavior / response to herbicide / eating behavior / response to zinc ion / response to corticosterone / dopamine biosynthetic process / amino acid binding / response to isolation stress / small molecule binding / cellular response to alkaloid / regulation of heart contraction / response to immobilization stress / smooth endoplasmic reticulum / response to light stimulus / response to electrical stimulus / social behavior / cellular response to manganese ion / response to salt stress / visual perception / ferric iron binding / cytoplasmic vesicle membrane / response to amphetamine / animal organ morphogenesis / response to activity / learning / response to nicotine / response to nutrient levels / locomotory behavior / cellular response to glucose stimulus / monooxygenase activity / ferrous iron binding / fatty acid metabolic process / oxygen binding / cerebral cortex development / response to peptide hormone / cellular response to nicotine / cellular response to growth factor stimulus / memory / cytoplasmic side of plasma membrane / cognition / cellular response to xenobiotic stimulus / terminal bouton / synaptic vesicle / response to estradiol / heart development / cytoplasmic vesicle / response to ethanol / response to lipopolysaccharide / perikaryon / response to hypoxia / 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
: / Tyrosine 3-monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsGoodwill, K.E. / Sabatier, C. / Stevens, R.C.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of tyrosine hydroxylase at 2.3 A and its implications for inherited neurodegenerative diseases.
Authors: Goodwill, K.E. / Sabatier, C. / Marks, C. / Raag, R. / Fitzpatrick, P.F. / Stevens, R.C.
History
DepositionJun 4, 1997Processing site: BNL
Revision 1.0Jun 3, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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

Downloads & links

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Assembly

Deposited unit
A: TYROSINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3302
Polymers39,2741
Non-polymers561
Water3,261181
1
A: TYROSINE HYDROXYLASE
hetero molecules

A: TYROSINE HYDROXYLASE
hetero molecules

A: TYROSINE HYDROXYLASE
hetero molecules

A: TYROSINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,3208
Polymers157,0964
Non-polymers2234
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 area10910 Å2
ΔGint-105 kcal/mol
Surface area54890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)189.323, 148.335, 57.975
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 HYDROXYLASE / TYROH


Mass: 39274.090 Da / Num. of mol.: 1
Fragment: CATALYTIC AND TETRAMERIZATION DOMAINS, RESIDUES 156 - 498
Source method: isolated from a genetically manipulated source
Details: FERRIC IRON AT THE ACTIVE SITE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.59 Å3/Da / Density % sol: 46 %
Description: THREE DERIVATIVES WITH ANOMALOUS DATE WERE USED.
Crystal growTemperature: 277 K / pH: 7.9
Details: 1.2 M AMMONIUM SULFATE 3.2% PEG 200 5% GLYCEROL 2 MM DTT 80 MM TRIS, PH 7.9 CRYSTALS GROWN AT 4 DEGREES C, temperature 277K
Crystal grow
*PLUS
Temperature: 4 K / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein11
2120 mMammonium sulfate11
3100 mMTris-HCl11
45 %glycerol11
52 mMdithiothreitol11
61.15 Mammonium sulfate12
73.2 %PEG20012
85 %glycerol12
980 mMTris-HCl12
102 mMdithiothreitol12

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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: Jun 1, 1996 / 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→30 Å / Num. obs: 18068 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 21.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 5 / Rsym value: 0.187 / % possible all: 92
Reflection
*PLUS
Num. measured all: 126857
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→37 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2194380.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1216 6.8 %RANDOM
Rwork0.2109 ---
obs0.2109 17787 96.6 %-
Solvent computationBsol: 42.71 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.169 Å20 Å20 Å2
2--14.769 Å20 Å2
3----23.938 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 1 181 2804
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
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_deg1.979
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_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.791.5
X-RAY DIFFRACTIONc_mcangle_it4.152
X-RAY DIFFRACTIONc_scbond_it4.292
X-RAY DIFFRACTIONc_scangle_it5.932.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 186 6.8 %
Rwork0.265 2530 -
obs--90.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
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_deg1.22
LS refinement shell
*PLUS
Rfactor obs: 0.265

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