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- PDB-2yct: Tyrosine phenol-lyase from Citrobacter freundii in complex with p... -

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Basic information

Entry
Database: PDB / ID: 2yct
TitleTyrosine phenol-lyase from Citrobacter freundii in complex with pyridine N-oxide and the quinonoid intermediate formed with L-alanine
ComponentsTYROSINE PHENOL-LYASE
KeywordsLYASE / PYRIDOXAL 5'-PHOSPHATE DEPENDENT ENZYME / BETA-ELIMINATION
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
PYRIDINE-N-OXIDE / : / Chem-PLI / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMilic, D. / Demidkina, T.V. / Faleev, N.G. / Phillips, R.S. / Matkovic-Calogovic, D. / Antson, A.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Crystallographic Snapshots of Tyrosine Phenol-Lyase Show that Substrate Strain Plays a Role in C-C Bond Cleavage
Authors: Milic, D. / Demidkina, T.V. / Faleev, N.G. / Phillips, R.S. / Matkovic-Calogovic, D. / Antson, A.A.
History
DepositionMar 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Mar 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 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 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_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_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)104,73112
Polymers103,1342
Non-polymers1,59710
Water14,250791
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)209,46224
Polymers206,2674
Non-polymers3,19520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area19920 Å2
ΔGint-75.2 kcal/mol
Surface area55680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.993, 143.770, 60.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 , 7 types, 801 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PLI / (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID


Mass: 318.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7P
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-9PO / PYRIDINE-N-OXIDE


Mass: 95.099 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5NO
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsRESIDUE LYS 257 IN CHAIN A IS PARTIALLY MODIFIED BY COVALENTLY BOUND PYRIDOXAL 5'-PHOSPHATE.

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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: 2.8 Å3/Da / Density % sol: 56.5 % / 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 ALANINE QUINONOID COMPLEX WITH PYRIDINE N-OXIDE (9PO) WAS PREPARED BY SOAKING WILD TYPE TPL CRYSTALS IN THE STABILIZATION SOLUTION CONTAINING 40% (W/V) POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER (PEG 5000 MME), 50 MM TRIETHANOLAMINE PH 8.0, 0.25 M KCL, 0.2 MM PYRIDOXAL 5-PHOSPHATE (PLP), 0.5 MM DITHIOTHREITOL (DTT), WITH ADDITION OF 100 MM L- ALANINE AND A SATURATING CONCENTRATION OF PYRIDINE N-OXIDE. SINCE THE CRYSTALS QUALITY DETERIORATED RAPIDLY, THE SOAKING TIME WAS RESTRICTED TO ABOUT 20 S.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 55230 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.5 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EZ2

2ez2


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.823 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1811 995 1.8 %RANDOM
Rwork0.13926 ---
obs0.14003 54235 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 101 791 8100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227534
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.96510157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77323.896367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.479151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9471552
X-RAY DIFFRACTIONr_chiral_restr0.0930.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215771
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.252.54557
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10447313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.13362977
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.656102844
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: 2.25→2.29 Å / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.229 45 -
Rwork0.17 2623 -
obs--94.48 %
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)
10.8060.2331-0.13151.1351-0.05570.6158-0.030.08090.0148-0.14850.0144-0.2286-0.08510.18970.01560.1207-0.01960.01950.10760.020.030524.1184.161-2.307
20.8588-0.3404-0.04750.9562-0.04820.4969-0.0667-0.1651-0.05920.16190.0346-0.17310.13290.15660.03210.16020.0598-0.01760.12750.03630.020920.31453.98918.135
31.97230.1710.14561.4842-0.13141.27130.0207-0.17290.0680.3266-0.0399-0.3063-0.08980.32770.01920.2826-0.0732-0.06460.2475-0.0110.142129.28891.88921.289
42.2517-1.1345-0.37662.2718-0.01030.81410.16610.1834-0.0067-0.2947-0.1411-0.1920.08610.1585-0.0250.19850.07720.02010.1084-0.01120.039920.79244.837-8.298
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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