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- PDB-3f6b: Crystal structure of benzoylformate decarboxylase in complex with... -

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Basic information

Entry
Database: PDB / ID: 3f6b
TitleCrystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / thiamin adduct / Aromatic hydrocarbons catabolism / Calcium / Decarboxylase / Magnesium / Mandelate pathway / Metal-binding / Thiamine pyrophosphate
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / acetolactate synthase activity / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains ...Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8PA / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsBrandt, G.S. / McLeish, M.J. / Kenyon, G.L. / Petsko, G.A. / Ringe, D. / Jordan, F.
CitationJournal: Biochemistry / Year: 2009
Title: Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.
Authors: Chakraborty, S. / Nemeria, N.S. / Balakrishnan, A. / Brandt, G.S. / Kneen, M.M. / Yep, A. / McLeish, M.J. / Kenyon, G.L. / Petsko, G.A. / Ringe, D. / Jordan, F.
History
DepositionNov 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.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.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_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
X: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6263
Polymers56,0431
Non-polymers5832
Water8,323462
1
X: Benzoylformate decarboxylase
hetero molecules

X: Benzoylformate decarboxylase
hetero molecules

X: Benzoylformate decarboxylase
hetero molecules

X: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,50412
Polymers224,1734
Non-polymers2,3318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area25050 Å2
ΔGint-132.6 kcal/mol
Surface area59880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.540, 96.070, 137.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11X-533-

HOH

21X-714-

HOH

31X-730-

HOH

41X-802-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFD / BFDC


Mass: 56043.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: DSM 291 / NCIB 9494 / NCTC 10936 / Stanier 90 / Gene: mdlC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-8PA / 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium


Mass: 558.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N5O8P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1. 8PA IS A COVALENT ADDUCT BETWEEN 3-(PYRIDIN-3-YL) ACRYLALDEHYDE AND THE THDP COFACTOR. 2. ...1. 8PA IS A COVALENT ADDUCT BETWEEN 3-(PYRIDIN-3-YL) ACRYLALDEHYDE AND THE THDP COFACTOR. 2. ACCORDING TO AUTHORS, BOTH RELATED ENTRIES 3F6B AND 3F6E HAVE THE SAME SUBSTRATE-COFACTOR ADDUCT. THESE STRUCTURES WERE SOLVED IN SUPPORT OF ENZYMOLOGICAL EXPERIMENTS WITH BENZOYLFORMATE DECARBOXYLASE. THE ENZYME DECARBOXYLATES THE 3-PKB SUBSTRATE TO GENERATE AN ALDEHYDE. THIS ALDEHYDE IS PAA, THE SUBSTRATE APPLIED IN THE EXPERIMENTS THAT GAVE RISE TO 3F6B STRUCTURE. WHEN AUTHORS CRYSTALLIZE THE ENZYME IN THE PRESENCE OF 3-PKB, THE SPECIES THAT IS GENERATED THAN TRAPPED IS PAA, VIA REACTION WITH THE THIAZOLIUM YLID OF THE THDP COFACTOR TO GENERATE THE ADDUCT SEEN IN BOTH STRUCTURES. THE 3-PKB INHIBITOR WAS DESIGNED FIRST, AND THEN PAA WAS DEVELOPED TO CHECK THE HYPOTHESIS THAT 3-PKB IS CONVERTED TO PAA IN THE ACTIVE SITE. INDEED, THE ADDUCT IS THE SAME IN 3F6B AND 3F6E.

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 150 mM CaCl2, 0.5% v/v MPD (2-methyl-2,4-pentanediol), 22% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 120069 / % possible obs: 95.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.089 / Χ2: 1.077 / Net I/σ(I): 16.911
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.34-1.393.80.61101280.90385.1
1.39-1.445.30.527113730.95795.9
1.44-1.516.20.42116651.198
1.51-1.596.40.317116531.13198.1
1.59-1.696.30.244117211.16998.1
1.69-1.826.10.183116641.15497.8
1.82-25.90.135114331.1395.8
2-2.296.20.109116661.05497.2
2.29-2.896.40.092117201.04397
2.89-506.40.056117241.01894.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BFD

1bfd


Resolution: 1.34→46.08 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.898 / SU B: 0.725 / SU ML: 0.03 / SU R Cruickshank DPI: 0.05 / SU Rfree: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 5750 5 %RANDOM
Rwork0.162 ---
all0.167 120069 --
obs0.163 114737 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.79 Å2 / Biso mean: 16.285 Å2 / Biso min: 2.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.34→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 37 462 4463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224100
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9725610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10224.451173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87915612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9541523
X-RAY DIFFRACTIONr_chiral_restr0.1360.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023178
X-RAY DIFFRACTIONr_nbd_refined0.2090.21850
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2308
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.2128
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.262
X-RAY DIFFRACTIONr_mcbond_it1.1331.52693
X-RAY DIFFRACTIONr_mcangle_it1.58124233
X-RAY DIFFRACTIONr_scbond_it2.71631597
X-RAY DIFFRACTIONr_scangle_it3.8744.51376
LS refinement shellResolution: 1.34→1.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 359 -
Rwork0.305 6731 -
all-7090 -
obs--80.51 %

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