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- PDB-1qpb: PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE -

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Basic information

Entry
Database: PDB / ID: 1qpb
TitlePYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE
ComponentsPYRUVATE DECARBOXYLASE (FORM B)
KeywordsLYASE / THIAMINE PYRUVATE / PYRUVAMIDE
Function / homology
Function and homology information


phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / glycolytic fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases ...phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / glycolytic fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / branched-chain amino acid catabolic process / tryptophan catabolic process / L-phenylalanine catabolic process / pyruvate metabolic process / thiamine pyrophosphate binding / magnesium ion binding / nucleus / cytoplasm / 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
PYRUVAMIDE / THIAMINE DIPHOSPHATE / Pyruvate decarboxylase isozyme 1
Similarity search - Component
Biological speciesSACCHAROMYCES PASTORIANUS (lager yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLu, G. / Dobritzsch, D. / Schneider, G.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: The Structural Basis of Substrate Activation in Yeast Pyruvate Decarboxylase a Crystallographic and Kinetic Study
Authors: Lu, G. / Dobritzsch, D. / Baumann, S. / Schneider, G. / Konig, S.
#1: Journal: FEBS Lett. / Year: 1997
Title: Novel Tetramer Assembly of Pyruvate Decarboxylase from Brewer'S Yeast Observed in a New Crystal Form
Authors: Lu, G. / Dobritzsch, D. / Konig, S. / Schneider, G.
History
DepositionNov 26, 1999Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 4, 2000ID: 1YPD
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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.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
Remark 650 HELIX DETERMINATION METHOD: DSSP
Remark 700 SHEET DETERMINATION METHOD: DSSP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRUVATE DECARBOXYLASE (FORM B)
B: PYRUVATE DECARBOXYLASE (FORM B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1848
Polymers123,1102
Non-polymers1,0736
Water2,540141
1
A: PYRUVATE DECARBOXYLASE (FORM B)
B: PYRUVATE DECARBOXYLASE (FORM B)
hetero molecules

A: PYRUVATE DECARBOXYLASE (FORM B)
B: PYRUVATE DECARBOXYLASE (FORM B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,36716
Polymers246,2204
Non-polymers2,14712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area19930 Å2
ΔGint-100.8 kcal/mol
Surface area91090 Å2
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-59.81 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.049, 119.700, 81.283
Angle α, β, γ (deg.)90.00, 120.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PYRUVATE DECARBOXYLASE (FORM B) / ALPHA-CARBOXYLASE / PYRUVIC DECARBOXYLASE / ALPHA-KETOACID CARBOXYLASE


Mass: 61555.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FORM B / Source: (natural) SACCHAROMYCES PASTORIANUS (lager yeast) / Strain: WEIHENSTEPHAN 34/70 (2124, BOHEMIAN LAGER) / References: UniProt: P06169, pyruvate decarboxylase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PYM / PYRUVAMIDE


Mass: 87.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 43 %
Crystal growpH: 5.8
Details: 8-14% PEG6000 20MM SODIUM CITRATE AT PH 5.7 1MM DTE, 5MM THDP, 5MM MGSO4
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMsodium citrate1drop
31 mMDTE1drop
45 mMThDP1drop
55 mM1dropMgSO4
6320 mMpyruvamide1drop
720 mMsodium citrate1reservoir
81 mMDTE1reservoir
95 mMThDP1reservoir
105 mM1reservoirMgSO4
1113-14 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1997
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 42140 / % possible obs: 88.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 33.0519 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.091 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5 / Rsym value: 0.38 / % possible all: 60
Reflection shell
*PLUS
% possible obs: 56 %

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Processing

Software
NameVersionClassification
CNS3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PVD

1pvd


Resolution: 2.4→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 15 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION WAS APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1724 4 %RANDOM
Rwork0.233 ---
obs0.233 42411 89 %-
Displacement parametersBiso mean: 31.0519 Å2
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8550 0 66 141 8757
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.38→2.42 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 25 0.46 %
Rwork0.363 540 -
obs--34.5 %
Software
*PLUS
Name: CNS / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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