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- PDB-2vlh: Quinonoid intermediate of Citrobacter freundii tyrosine phenol-ly... -

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Basic information

Entry
Database: PDB / ID: 2vlh
TitleQuinonoid intermediate of Citrobacter freundii tyrosine phenol-lyase formed with methionine
ComponentsTYROSINE PHENOL-LYASE
KeywordsLYASE / PLP-DEPENDENT ENZYME / QUINONOID INTERMEDIATE / PYRIDOXAL PHOSPHATE / TYROSINE DEGRADATION
Function / homology
Function and homology information


tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process
Similarity search - Function
Tyrosine phenol-lyase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Tyrosine phenol-lyase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Chem-PM9 / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMilic, D. / Demidkina, T.V. / Matkovic-Calogovic, D. / Antson, A.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Insights Into the Catalytic Mechanism of Tyrosine Phenol-Lyase from X-Ray Structures of Quinonoid Intermediates.
Authors: Milic, D. / Demidkina, T.V. / Faleev, N.G. / Matkovic-Calogovic, D. / Antson, A.A.
History
DepositionJan 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 2, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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 PHENOL-LYASE
B: TYROSINE PHENOL-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3148
Polymers103,1342
Non-polymers1,1806
Water15,979887
1
A: TYROSINE PHENOL-LYASE
B: TYROSINE PHENOL-LYASE
hetero molecules

A: TYROSINE PHENOL-LYASE
B: TYROSINE PHENOL-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,62816
Polymers206,2674
Non-polymers2,36012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area19070 Å2
ΔGint-79.2 kcal/mol
Surface area68960 Å2
MethodPQS
Unit cell
Length a, b, c (Å)132.886, 143.284, 59.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2036-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TYROSINE PHENOL-LYASE / BETA-TYROSINASE


Mass: 51566.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Plasmid: PTZTPL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SVS 370 / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 6 types, 893 molecules

#2: Chemical ChemComp-PM9 / (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}-4-(METHYLSULFANYL)BUTANOIC ACID


Mass: 378.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O7PS
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details2-(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-1H-PYRIDIN-4-YLIDENEMETHY 3,6,9,12,15,18-HEXAOXAICOSANE- ...2-(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-1H-PYRIDIN-4-YLIDENEMETHY 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL (P33): A PART OF A PEG CHAIN TRIETHYLENE GLYCOL (PGE): A PART OF A PEG CHAIN

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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: 2.76 Å3/Da / Density % sol: 55.4 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALS OF THE C. FREUNDII TPL WERE GROWN AT 277 AND 293 K USING THE HANGING DROP VAPOR DIFFUSION METHOD. THE BEST CRYSTALS WERE OBTAINED BY MIXING 2 UL OF THE PROTEIN SOLUTION (18-20 MG/ML) ...Details: CRYSTALS OF THE C. FREUNDII TPL WERE GROWN AT 277 AND 293 K USING THE HANGING DROP VAPOR DIFFUSION METHOD. THE BEST CRYSTALS WERE OBTAINED BY MIXING 2 UL OF THE PROTEIN SOLUTION (18-20 MG/ML) CONTAINING 50MM K-PHOSPHATE PH 8.0, 0.5 MM PLP, 1MM DDT WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 50 MM TRIETHANOLAMINE BUFFER (PH 8.0), 0.5 MM PLP, 2 MM DDT, 0.4 M KCL, AND 35-38% (W/V) POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER. THE INTERMEDIATE WITH METHIONINE WAS PREPARED BY SOAKING THE TPL CRYSTALS FOR 5 MIN IN THE STABILIZATION SOLUTION CONTAINING 40% POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER, 50 MM TRIETHANOLAMINE BUFFER (PH 8.0), 0.25 M KCL, 0.2 MM PLP, 0.5 MM DTT AND 70 MM L-METHIONINE. CRYSTALS WERE FROZEN DIRECTLY FROM THE SOAKING SOLUTION.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 29, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 76260 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EZ2

2ez2


Resolution: 1.95→97.59 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.234 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1058 1.4 %RANDOM
Rwork0.155 ---
obs0.156 75067 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---1.01 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→97.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 73 887 8184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227508
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.96110119
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96723.88366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.578151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6631552
X-RAY DIFFRACTIONr_chiral_restr0.0970.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025732
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.24118
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25191
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2824
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.2138
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3122.54558
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10547317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.05562998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.71102799
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.02 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.227 116
Rwork0.192 7386
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)
10.67670.2528-0.15091.2482-0.07920.5848-0.01380.06610.0148-0.1462-0.0127-0.2287-0.08130.16470.0265-0.1397-0.02460.0055-0.11540.026-0.14623.91383.925-2.213
20.7841-0.40440.14141.1603-0.00170.6565-0.0465-0.136-0.05660.21960.0412-0.16370.12570.11940.0053-0.10720.0358-0.028-0.11150.0166-0.157320.18353.82217.994
31.695-0.11980.97951.7167-0.02541.4775-0.0034-0.17070.11430.3451-0.0615-0.3377-0.08130.3430.0650.0486-0.0838-0.08310.03510.00760.033829.10891.50721.242
41.9074-1.0099-0.41862.53110.07061.27250.07450.1055-0.0175-0.1593-0.0378-0.27130.12040.2037-0.0367-0.09910.05680.0055-0.1011-0.0304-0.121920.7544.763-8.176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION1A45 - 345
3X-RAY DIFFRACTION1A405 - 422
4X-RAY DIFFRACTION2B1 - 13
5X-RAY DIFFRACTION2B45 - 345
6X-RAY DIFFRACTION2B405 - 422
7X-RAY DIFFRACTION3A19 - 44
8X-RAY DIFFRACTION3A346 - 404
9X-RAY DIFFRACTION3A434 - 456
10X-RAY DIFFRACTION4B19 - 44
11X-RAY DIFFRACTION4B346 - 404
12X-RAY DIFFRACTION4B434 - 456

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