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- PDB-2xsn: Crystal Structure of Human Tyrosine Hydroxylase Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 2xsn
TitleCrystal Structure of Human Tyrosine Hydroxylase Catalytic Domain
ComponentsTYROSINE 3-MONOOXYGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / phytoalexin metabolic process / dopamine biosynthetic process from tyrosine / phthalate metabolic process / glycoside metabolic process / terpene metabolic process / isoquinoline alkaloid metabolic process / norepinephrine biosynthetic process / embryonic camera-type eye morphogenesis ...tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / phytoalexin metabolic process / dopamine biosynthetic process from tyrosine / phthalate metabolic process / glycoside metabolic process / terpene metabolic process / isoquinoline alkaloid metabolic process / norepinephrine biosynthetic process / embryonic camera-type eye morphogenesis / hyaloid vascular plexus regression / circadian sleep/wake cycle / epinephrine biosynthetic process / Catecholamine biosynthesis / aminergic neurotransmitter loading into synaptic vesicle / dopamine binding / response to pyrethroid / eye photoreceptor cell development / response to isolation stress / melanosome membrane / sphingolipid metabolic process / response to ether / synaptic transmission, dopaminergic / tetrahydrobiopterin binding / response to herbicide / mating behavior / dopamine biosynthetic process / amino acid binding / regulation of heart contraction / eating behavior / pigmentation / response to corticosterone / response to zinc ion / cellular response to alkaloid / social behavior / response to immobilization stress / smooth endoplasmic reticulum / response to light stimulus / anatomical structure morphogenesis / cellular response to manganese ion / response to electrical stimulus / heart morphogenesis / response to salt stress / response to amphetamine / visual perception / response to nutrient levels / ferric iron binding / fatty acid metabolic process / learning / response to activity / locomotory behavior / cellular response to glucose stimulus / animal organ morphogenesis / ferrous iron binding / terminal bouton / cytoplasmic side of plasma membrane / cerebral cortex development / memory / cellular response to growth factor stimulus / response to peptide hormone / oxygen binding / cellular response to nicotine / cellular response to xenobiotic stimulus / synaptic vesicle / response to estradiol / heart development / cytoplasmic vesicle / perikaryon / response to ethanol / response to lipopolysaccharide / response to hypoxia / neuron projection / protein domain specific binding / axon / dendrite / perinuclear region of cytoplasm / enzyme binding / mitochondrion / identical protein binding / nucleus / cytoplasm / cytosol
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsMuniz, J.R.C. / Cooper, C.D.O. / Yue, W.W. / Krysztofinska, E. / von Delft, F. / Knapp, S. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Muniz, J.R.C. / Cooper, C.D.O. / Yue, W.W. / Krysztofinska, E. / von Delft, F. / Knapp, S. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Kavanagh, K.L. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Tyrosine Hydroxylase Catalytic Domain
Authors: Muniz, J.R.C. / Cooper, C.D.O. / Yue, W.W. / Krysztofinska, E. / von Delft, F. / Knapp, S. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Kavanagh, K.L. / Oppermann, U.
History
DepositionOct 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Source and taxonomy ...Database references / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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

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Assembly

Deposited unit
A: TYROSINE 3-MONOOXYGENASE
B: TYROSINE 3-MONOOXYGENASE
C: TYROSINE 3-MONOOXYGENASE
D: TYROSINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,6018
Polymers156,3404
Non-polymers2624
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-203.8 kcal/mol
Surface area55070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.420, 191.420, 168.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4597, 0.8873, 0.0364), (0.013, 0.0283), (0.0263, -0.9993)
Vector: 34.9042, 49.6818, 31.9241)

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Components

#1: Protein
TYROSINE 3-MONOOXYGENASE / TYROSINE 3-HYDROXYLASE / TH


Mass: 39084.887 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 193-528 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PL / References: UniProt: P07101, tyrosine 3-monooxygenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 193 TO MET ENGINEERED RESIDUE IN CHAIN B, LYS 193 TO MET ...ENGINEERED RESIDUE IN CHAIN A, LYS 193 TO MET ENGINEERED RESIDUE IN CHAIN B, LYS 193 TO MET ENGINEERED RESIDUE IN CHAIN C, LYS 193 TO MET ENGINEERED RESIDUE IN CHAIN D, LYS 193 TO MET

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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: 2.85 Å3/Da / Density % sol: 56.92 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM ACETATE, 0.1 M TRI-SODIUM CITRATE, 30% PEG 4K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.68→63.12 Å / Num. obs: 51392 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Biso Wilson estimate: 67.81 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.2
Reflection shellResolution: 2.68→2.82 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→62.66 Å / Cor.coef. Fo:Fc: 0.9366 / Cor.coef. Fo:Fc free: 0.9182 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 2608 5.1 %RANDOM
Rwork0.1893 ---
obs0.1909 51346 100 %-
Displacement parametersBiso mean: 54.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.3137 Å20 Å20 Å2
2--0.3137 Å20 Å2
3----0.6275 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: LAST / Resolution: 2.68→62.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10661 0 4 227 10892
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111004HARMONIC2
X-RAY DIFFRACTIONt_angle_deg114948HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5011SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes266HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1634HARMONIC5
X-RAY DIFFRACTIONt_it11004HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion2.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1383SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12520SEMIHARMONIC4
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3004 185 4.96 %
Rwork0.2319 3544 -
all0.2352 3729 -
obs--100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodOrigin x (Å)Origin y (Å)Origin z (Å)L11 (°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)
1refined66.06562.738617.3908
2refined58.4719.808326.42261.3412-0.3932-0.76392.21040.7762.1367-0.05640.4775-0.1716-0.43550.00130.19990.0166-0.41290.0551-0.09660.0190.019-0.0212-0.028-0.0795
3refined46.966611.328724.70791.7335-0.008-1.20931.7879-0.05081.9495-0.03920.4441-0.2086-0.18890.04750.1531-0.1371-0.7052-0.0082-0.12830.0778-0.0190.0492-0.0112-0.0468
4refined70.168731.701731.05453.1046-0.94790.10241.799-0.29531.84060.08630.23520.0237-0.1963-0.08910.6386-0.072-0.66410.0028-0.17870.0719-0.03120.08930.0029-0.0058
5refined28.430558.653535.42180.8078-1.83950.26764.0674-1.00993.2969-0.04770.08180.2041-0.02710.007-0.5044-0.0035-0.0660.0407-0.05810.10350.0499-0.10650.05640.0307
6refined42.731556.532140.21991.2418-0.2980.05610.8891-0.19680.97980.0371-0.3793-0.07330.28020.04470.05340.2087-0.3396-0.0818-0.0712-0.0151-0.00670.04150.044-0.1103
7refined33.506852.189730.95882.515-1.4520.8107-2.515-0.164400.0278-0.116-0.0392-0.02980.0474-0.1946-0.01570.0185-0.0753-0.02930.0847-0.04510.01720.0706-0.0076
8refined30.955537.085829.44451.0011-0.4852-0.36081.02090.11362.17150.0215-0.1299-0.330.11820.0234-0.04050.5934-0.2793-0.0449-0.0275-0.018-0.0673-0.07460.0366-0.0198
9refined60.550447.984826.01611.75720.22980.0163.74770.36781.94250.01660.132-0.59220.00390.0971-0.06270.7403-0.2011-0.11370.054-0.0995-0.1167-0.18210.05620.0041
10refined60.801974.471637.82142.1873-1.4967-0.92772.0823-0.36312.23630.16160.07230.2817-0.377-0.2519-0.4015-0.0957-0.20460.09030.0580.0818-0.0133-0.19420.01380.0132
11refined67.939574.926734.48721.03670.49620.09444.0467-0.84591.18420.07390.22020.1670.0170.0297-0.1561-0.16150.1368-0.1036-0.1430.10410.0079-0.1162-0.0211-0.0067
12refined75.673665.885836.23232.7991-1.9268-1.6310.40550.53654.3136-0.05-0.01250.20320.089-0.0511-0.18130.02290.13940.1012-0.16190.09820.07690.01780.04730.1403
13refined82.162563.018336.88321.5850.7788-0.67512.3459-0.61970.28060.20550.1373-0.1957-0.1276-0.0254-0.7360.10710.6002-0.1801-0.22950.09260.0343-0.0233-0.07490.1532
14refined57.126645.1730.62026.42220.03811.2435-0.31580.75944.40850.15220.0967-0.1588-0.0366-0.4217-0.55030.11130.56380.2695-0.34660.12650.0039-0.1417-0.0050.3037
15refined97.778918.467610.86320.7529-1.55060.24073.2198-2.41110.63520.0420.06120.1413-0.051-0.1584-0.15460.2176-0.03860.1164-0.09320.0886-0.0171-0.0769-0.00380.0148
16refined100.471423.899233.49134.98120.2347-1.29890.817-0.85891.76570.12480.2217-0.49390.0866-0.1891-0.2054-0.25750.15920.06430.00250.00120.0704-0.249-0.03410.0043
17refined92.524824.8319.8551-0.52910.17871.54881.98561.67497.04270.0056-0.4896-0.01120.36380.0394-0.1652-0.1980.0191-0.0450.0781-0.26790.0650.06990.0337-0.2543
18refined96.172438.094621.24964.6036-0.4393-0.142.0002-0.86511.86470.2655-0.40970.4720.1834-0.1758-0.1695-0.38520.2221-0.0897-0.045-0.02340.1212-0.1936-0.0025-0.0249
19refined101.479344.076621.4186.2219-0.31890.55134.2685-0.40050.03210.2034-0.34180.60450.2285-0.0527-0.1169-0.24710.0071-0.1507-0.0475-0.1010.2076-0.2818-0.05560.2666
20refined82.189543.396819.61231.53193.56713.49434.1343-0.231600.0487-0.17560.24830.123-0.09040.0141-0.18310.36120.0417-0.0905-0.21530.1657-0.1928-0.07990.2617
21refined66.062829.67827.30.29220.7645-0.87945.9143-2.89390.4542-0.0040.12310.3773-0.07520.1375-0.0325-0.097-0.0932-0.13350.20040.15050.2068-0.2956-0.05610.304
220.3801-0.9054-0.12032.1359-0.07321.01980.07330.21140.1262-0.3129-0.2919-0.0838-0.0856-0.0690.2186-0.03390.07620.0406-0.12740.0275-0.0129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A 233 - A 350)
2X-RAY DIFFRACTION2(A 351 - A 401)
3X-RAY DIFFRACTION3(A 402 - A 483)
4X-RAY DIFFRACTION4(A 484 - A 527)
5X-RAY DIFFRACTION5(B 193 - B 303)
6X-RAY DIFFRACTION6(B 304 - B 317)
7X-RAY DIFFRACTION7(B 318 - B 391)
8X-RAY DIFFRACTION8(B 392 - B 484)
9X-RAY DIFFRACTION9(B 485 - B 528)
10X-RAY DIFFRACTION10(C 193 - C 349)
11X-RAY DIFFRACTION11(C 350 - C 373)
12X-RAY DIFFRACTION12(C 374 - C 434)
13X-RAY DIFFRACTION13(C 435 - C 482)
14X-RAY DIFFRACTION14(C 483 - C 535)
15X-RAY DIFFRACTION15(D 194 - D 264)
16X-RAY DIFFRACTION16(D 265 - D 298)
17X-RAY DIFFRACTION17(D 299 - D 389)
18X-RAY DIFFRACTION18(D 390 - D 428)
19X-RAY DIFFRACTION19(D 429 - D 465)
20X-RAY DIFFRACTION20(D 466 - D 486)
21X-RAY DIFFRACTION21(D 487 - D 535)

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