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- PDB-2vjy: Pyruvate decarboxylase from Kluyveromyces lactis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2vjy
TitlePyruvate decarboxylase from Kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate
ComponentsPYRUVATE DECARBOXYLASE
KeywordsLYASE / METAL-BINDING / DECARBOXYLASE / DIMER OF DIMERS / METHYLACETYLPHOSPHONATE / METHYL ACETYLPHOSPHONATE / SUBSTRATE ACTIVATION / THIAMINE DIPHOSPHATE / THIAMINE PYROPHOSPHATE / ASYMMETRIC ACTIVE SITES / MAP / PYRUVATE / MAGNESIUM / FLAVOPROTEIN
Function / homology
Function and homology information


pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / nucleus / cytosol
Similarity search - Function
: / Thiamine pyrophosphate (TPP)-dependent 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 (TPP)-dependent 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
methoxy-[(1~{R})-1-oxidanylethyl]phosphinic acid / METHYL HYDROGEN (S)-ACETYLPHOSPHONATE / THIAMINE DIPHOSPHATE / Pyruvate decarboxylase
Similarity search - Component
Biological speciesKLUYVEROMYCES LACTIS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKutter, S. / Wille, G. / Weiss, M.S. / Konig, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
Authors: Kutter, S. / Weiss, M.S. / Wille, G. / Golbik, R. / Spinka, M. / Konig, S.
History
DepositionDec 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 2.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.3Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.5Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 2.6Dec 13, 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.ptnr1_label_seq_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
Revision 2.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
C: PYRUVATE DECARBOXYLASE
D: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,20023
Polymers246,8674
Non-polymers3,33319
Water18,8801048
1
A: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,16912
Polymers123,4342
Non-polymers1,73610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-57.8 kcal/mol
Surface area44730 Å2
MethodPQS
2
C: PYRUVATE DECARBOXYLASE
D: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,03111
Polymers123,4342
Non-polymers1,5989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-55.6 kcal/mol
Surface area44370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.760, 135.770, 107.260
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PYRUVATE DECARBOXYLASE


Mass: 61716.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast) / References: UniProt: Q12629, pyruvate decarboxylase

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Non-polymers , 5 types, 1067 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ALK / methoxy-[(1~{R})-1-oxidanylethyl]phosphinic acid


Mass: 140.075 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H9O4P
#5: Chemical ChemComp-ALU / METHYL HYDROGEN (S)-ACETYLPHOSPHONATE


Mass: 138.059 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7O4P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1048 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.68 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 20MM CITRATE, 10% PEG2000, 10% PEG6000, 5MM TDP, 5MM MAGNESIUM SULFATE, 1MM DTT, 40MM METHYL ACETYLPHOSPHONATE, PH 6.1, 0.95MG KLPDC/ML, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.93001
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93001 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. obs: 100426 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREP- AUTO MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G1I

2g1i
PDB Unreleased entry


Resolution: 2.3→20.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1006 1 %RANDOM
Rwork0.154 ---
obs0.154 99345 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.69 Å2
2--0.62 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17344 0 196 1048 18588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02217903
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.97124386
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21852244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64625760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.718152936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3351572
X-RAY DIFFRACTIONr_chiral_restr0.1670.22804
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.29229
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.212293
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.21260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.0270.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2631.511180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.033218100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.82836723
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2554.56286
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 83 -
Rwork0.192 7228 -
obs--99.85 %

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