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- PDB-2vk4: Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis -

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Basic information

Entry
Database: PDB / ID: 2vk4
TitleCrystal structure of pyruvate decarboxylase from Kluyveromyces lactis
ComponentsPYRUVATE DECARBOXYLASE
KeywordsLYASE / METAL-BINDING / DECARBOXYLASE / DIMER OF DIMERS / SUBSTRATE ACTIVATION / THIAMINE DIPHOSPHATE / TDP / TPP / MAGNESIUM / FLAVOPROTEIN / THIAMINE PYROPHOSPHATE / ASYMMETRIC ACTIVE SITES
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
THIAMINE DIPHOSPHATE / Pyruvate decarboxylase
Similarity search - Component
Biological speciesKLUYVEROMYCES LACTIS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKutter, S. / Relle, S. / Wille, G. / Weiss, M.S. / Konig, S.
Citation
Journal: J.Mol.Catal., B Enzym. / Year: 2014
Title: Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story.
Authors: Konig, S. / Spinka, M. / Kutter, S.
#1: Journal: FEBS J. / Year: 2006
Title: The Crystal Structure of Pyruvate Decarboxylase from Kluyveromyces Lactis. Implications for the Substrate Activation Mechanism of This Enzyme.
Authors: Kutter, S. / Wille, G. / Relle, S. / Weiss, M.S. / Hubner, G. / Konig, S.
History
DepositionDec 17, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionJan 27, 2009ID: 2G1I
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 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Dec 13, 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_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.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.ptnr1_label_seq_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: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
C: PYRUVATE DECARBOXYLASE
D: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,66612
Polymers246,8674
Non-polymers1,7988
Water23,7621319
1
A: PYRUVATE DECARBOXYLASE
B: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3336
Polymers123,4342
Non-polymers8994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-64.4 kcal/mol
Surface area46700 Å2
MethodPQS
2
C: PYRUVATE DECARBOXYLASE
D: PYRUVATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3336
Polymers123,4342
Non-polymers8994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-59.4 kcal/mol
Surface area46650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.709, 203.175, 79.815
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1319 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.59 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.45
Details: 50MM MES, 1MM DTT, 5MM TDP, 5MM MAGNESIUM SULFATE, 10% PEG 2000, 10% PEG 8000, 2MG KLPDC/ML, PH 6.45, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8125
DetectorType: MARRESEARCH / Detector: CCD / Date: May 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8125 Å / Relative weight: 1
ReflectionResolution: 1.95→48.45 Å / Num. obs: 155315 / % possible obs: 86.3 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 80.6

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Processing

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

2g1i
PDB Unreleased entry


Resolution: 1.95→48.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 7784 5 %RANDOM
Rwork0.178 ---
obs0.18 147446 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.06 Å2
2--0.26 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17227 0 108 1319 18654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02217699
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.851.96624105
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59652224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34624.974756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.696152909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7031572
X-RAY DIFFRACTIONr_chiral_restr0.4410.22778
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.28824
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.212166
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.21381
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.511096
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.588217960
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.51236603
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7724.56145
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 505
Rwork0.242 10144

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