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- PDB-2ycn: Y71F mutant of tyrosine phenol-lyase from Citrobacter freundii in... -

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Basic information

Entry
Database: PDB / ID: 2ycn
TitleY71F mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine
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
: / Chem-P61 / DI(HYDROXYETHYL)ETHER / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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.pdbx_dist_value / _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)104,3378
Polymers103,1022
Non-polymers1,2356
Water13,421745
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)208,67316
Polymers206,2034
Non-polymers2,47012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area20090 Å2
ΔGint-50.1 kcal/mol
Surface area55310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.635, 144.397, 59.660
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
11A-2032-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 51550.785 Da / Num. of mol.: 2 / Mutation: YES
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 , 5 types, 751 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-P61 / (2E)-3-(3-fluoro-4-hydroxyphenyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}propanoic acid


Mass: 428.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18FN2O8P
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 71 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 71 TO PHE

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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 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALS 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 50 MM K- ...Details: CRYSTALS 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 50 MM K-PHOSPHATE PH 8.0, 0.5 MM PLP, 1 MM 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. COMPLEX OF Y71F TPL WITH 3-FLUORO-L-TYROSINE WAS PREPARED BY SOAKING CRYSTALS IN THE STABILIZING SOLUTION CONTAINING 10 MM 3- FLUORO-L-TYROSINE FOR ABOUT 30 SECONDS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.04→17 Å / Num. obs: 71319 / % possible obs: 96 % / Observed criterion σ(I): -10 / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.7
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.2 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EZ2

2ez2


Resolution: 2.04→98.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.459 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE A 600 IS DISORDERED AND FOUND IN TWO CONFORMATIONS. A MAJOR PROPORTION OF ACTIVE SITE A IS OCCUPIED BY THE QUINONOID MOLECULE IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE A 600 IS DISORDERED AND FOUND IN TWO CONFORMATIONS. A MAJOR PROPORTION OF ACTIVE SITE A IS OCCUPIED BY THE QUINONOID MOLECULE IN THE TENSE STATE WITH OCCUPANCY ESTIMATED AT 0.67. THE RESIDUAL ELECTRON DENSITY SUGGESTS THAT A MINOR POPULATION OF SUBUNIT A IS IN THE OPEN CONFORMATION. DUE TO THE UNCONNECTED PEAKS IN THE ELECTRON DENSITY MAPS AND THE LOW OCCUPANCY, IT WAS NOT POSSIBLE TO MODEL THIS OPEN CONFORMATION. THE ELECTRON DENSITY IN THE ACTIVE SITE OF SUBUNIT A INDICATES THAT APART FROM THE TENSE QUINONOID THERE IS AN ADDITIONAL CHEMICAL SPECIES. THE RESIDUAL ELECTRON DENSITY IS BEST FITTED BY RELAXED QUINONOID MODELED WITH THE ESTIMATED OCCUPANCY OF 0.33 IN THE SAME GEOMETRY AS IN THE OPEN ACTIVE SITE B
RfactorNum. reflection% reflectionSelection details
Rfree0.20886 1047 1.5 %RANDOM
Rwork0.16339 ---
obs0.16405 70272 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---1.21 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2.04→98.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7222 0 80 745 8047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227539
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.96610167
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21123.804368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.819151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0931554
X-RAY DIFFRACTIONr_chiral_restr0.0970.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215788
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_it1.382.54563
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18847320
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.08762976
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.667102842
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: 2.038→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 69 -
Rwork0.201 4251 -
obs--79.09 %
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)
11.23980.8299-0.0562.01390.02710.6512-0.15160.1834-0.078-0.32320.1345-0.4153-0.08040.21890.01710.1539-0.05070.05260.21140.0210.09123.82484.784-2.336
21.0652-0.5425-0.0131.86560.11180.655-0.1135-0.1829-0.07220.39620.0652-0.28480.15270.2050.04830.17980.0709-0.06040.18920.04850.055320.30354.4418.09
32.6410.31451.02743.8166-0.44191.21020.0473-0.18640.0690.9184-0.2227-0.8387-0.18760.43650.17540.3981-0.1682-0.20280.34460.05180.296728.97492.49421.277
43.2171-2.7917-0.86254.74040.491.260.35850.26390.1332-0.6776-0.3092-0.54110.07240.221-0.04920.23060.13460.05770.20290.00570.079321.25345.16-7.929
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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