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- PDB-2yii: Manipulating the regioselectivity of phenylalanine aminomutase: n... -

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Basic information

Entry
Database: PDB / ID: 2yii
TitleManipulating the regioselectivity of phenylalanine aminomutase: new insights into the reaction mechanism of MIO-dependent enzymes from structure-guided directed evolution
ComponentsPHENYLALANINE AMMONIA-LYASE
KeywordsLYASE
Function / homology
Function and homology information


phenylalanine aminomutase (L-beta-phenylalanine forming) / intramolecular aminotransferase activity / paclitaxel biosynthetic process / phenylalanine ammonia-lyase / L-phenylalanine metabolic process / cinnamic acid biosynthetic process / alkaloid biosynthetic process / phenylalanine ammonia-lyase activity / L-phenylalanine catabolic process / protein homotetramerization / cytoplasm
Similarity search - Function
Phenylalanine aminomutase (L-beta-phenylalanine forming) / Phenylalanine ammonia-lyase 1; domain 3 / Phenylalanine ammonia-lyase / Phenylalanine ammonia-lyase, shielding domain superfamily / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Enzyme I; Chain A, domain 2 / Fumarase/aspartase (N-terminal domain) ...Phenylalanine aminomutase (L-beta-phenylalanine forming) / Phenylalanine ammonia-lyase 1; domain 3 / Phenylalanine ammonia-lyase / Phenylalanine ammonia-lyase, shielding domain superfamily / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Enzyme I; Chain A, domain 2 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FORMIC ACID / Phenylalanine aminomutase (L-beta-phenylalanine forming)
Similarity search - Component
Biological speciesTAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWu, B. / Szymanski, W. / Wybenga, G.G. / Heberling, M.M. / Bartsch, S. / Wildeman, S. / Poelarends, G.J. / Feringa, B.L. / Dijkstra, B.W. / Janssen, D.B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Mechanism-Inspired Engineering of Phenylalanine Aminomutase for Enhanced Beta-Regioselective Asymmetric Amination of Cinnamates.
Authors: Wu, B. / Szymanski, W. / Wybenga, G.G. / Heberling, M.M. / Bartsch, S. / De Wildeman, S. / Poelarends, G.J. / Feringa, B.L. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionMay 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHENYLALANINE AMMONIA-LYASE
B: PHENYLALANINE AMMONIA-LYASE
C: PHENYLALANINE AMMONIA-LYASE
D: PHENYLALANINE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,11617
Polymers310,2154
Non-polymers90113
Water15,025834
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39470 Å2
ΔGint-172.5 kcal/mol
Surface area71690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.454, 145.999, 99.680
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1167, -0.2364, 0.9646), (-0.2405, -0.9356, -0.2584), (0.9636, -0.2621, 0.0524)20.75, 139.7, 15.52
2given(-0.9999, -0.01034, -0.001407), (-0.009757, 0.8783, 0.478), (-0.003708, 0.478, -0.8784)137.1, -26.58, 107.2
3given(0.1192, 0.251, -0.9606), (0.2495, -0.9441, -0.2157), (-0.961, -0.2139, -0.1752)114.5, 103.6, 160.3

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Components

#1: Protein
PHENYLALANINE AMMONIA-LYASE / / PHENYLALANINE AMINOMUTASE


Mass: 77553.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: THIOESTER BOND BETWEEN THE MDO PROSTHETIC GROUP AND A MOLECULE OF BETA-MERCAPTOETHANOL, DISULFIDE BRIDGE BETWEEN RESIDUE C89 AND A BETA-MERCAPTOETHANOL MOLECULE, COVALENT BOND BETWEEN MDO 175 AND RESIDUE D178
Source: (gene. exp.) TAXUS WALLICHIANA VAR. CHINENSIS (Chinese yew)
Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TOP10
References: UniProt: Q68G84, EC: 5.4.3.-, phenylalanine ammonia-lyase
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 834 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 % / Description: NONE
Crystal growDetails: 4% TACSIMATE PH 6.0, 12% W/V PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.18→48.67 Å / Num. obs: 142853 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1W27 AND 1Y2M

1w27

1y2m


Resolution: 2.18→98.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.134 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 7140 5 %RANDOM
Rwork0.17875 ---
obs0.18053 135680 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.037 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å21.56 Å2
2---0.21 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.18→98.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20081 0 50 834 20965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02220468
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.98327707
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19752555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91323.915871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.619153559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.72215149
X-RAY DIFFRACTIONr_chiral_restr0.0730.23271
X-RAY DIFFRACTIONr_gen_planes_refined
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_it0.3681.512885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.702220740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.05237583
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7724.56967
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: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 465 -
Rwork0.239 9144 -
obs--89.34 %

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