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- PDB-1pyd: CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYR... -

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Entry
Database: PDB / ID: 1pyd
TitleCATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION
ComponentsPYRUVATE DECARBOXYLASE
KeywordsLYASE(CARBON-CARBON)
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
THIAMINE DIPHOSPHATE / Pyruvate decarboxylase isozyme 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsFurey, W. / Dyda, F.
Citation
Journal: Biochemistry / Year: 1993
Title: Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution.
Authors: Dyda, F. / Furey, W. / Swaminathan, S. / Sax, M. / Farrenkopf, B. / Jordan, F.
#1: Journal: Biochemistry and Physiology of Thiamin Diphosphate Enzymes
Year: 1991
Title: Multiple Crystal Forms of Brewers' Yeast Pyruvate Decarboxylase: Characterization and Preliminary Crystallographic Analysis
Authors: Dyda, F. / Furey, W. / Swaminathan, S. / Sax, M. / Jordan, F. / Farrenkopf, B.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Preliminary Crystallographic Data for the Thiamin Diphosphate-Dependent Enzyme Pyruvate Decarboxylase from Brewers' Yeast
Authors: Dyda, F. / Furey, W. / Swaminathan, S. / Sax, M. / Farrenkopf, B. / Jordan, F.
History
DepositionMar 23, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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 / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6446
Polymers121,7452
Non-polymers8994
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-52 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.950, 74.670, 119.950
Angle α, β, γ (deg.)90.00, 116.39, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.91229, -0.04516, -0.40704), (-0.04516, -0.97675, 0.20958), (-0.40704, 0.20958, 0.88904)
Vector: 2.164, -1.492, 0.632)
DetailsTHE UNIT CELL CONTAINS TWO TETRAMERS, WITH ONE DIMER IN THE ASYMMETRIC UNIT. IN TERMS OF THE CRYSTAL AXES, THE TWO MONOMERS IN THE ASYMMETRIC UNIT (CHAINS *A* AND *B*) ARE RELATED BY A NONCRYSTALLOGRAPHIC TWO-FOLD AXIS INCLINED BY 83.31 DEGREES TO THE B AXIS, AND WHOSE PROJECTION ON THE AC PLANE MAKES ANGLES OF 102.16 DEGREES WITH THE A AXIS AND 14.23 DEGREES WITH THE C AXIS. THIS TRANSFORMATION IS PRESENTED ON *MTRIX* RECORDS BELOW. THE COMPLETE TETRAMER IS FORMED BY THE SUBMITTED DIMER AND ITS CRYSTALLOGRAPHICALLY RELATED MATE OBTAINED BY TWO-FOLD ROTATION ABOUT THE B AXIS. THE NONCRYSTALLOGRAPHIC TWO-FOLD AXIS DOES NOT INTERSECT THE B AXIS, AS ITS CLOSEST APPROACH IS OFFSET BY 1.352 ANGSTROMS. THE TETRAMER THUS HAS ONLY APPROXIMATE 222 SYMMETRY, AS IT MUST INTERSECT THE B AXIS AND BE INCLINED TO IT BY 90 DEGREES FOR EXACT 222 SYMMETRY.

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Components

#1: Protein PYRUVATE DECARBOXYLASE


Mass: 60872.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P06169, pyruvate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CATALYTIC CENTERS ARE LOCATED AT THE INTERFACE BETWEEN MONOMERS WITHIN EACH DIMER, WITH TWO ...THE CATALYTIC CENTERS ARE LOCATED AT THE INTERFACE BETWEEN MONOMERS WITHIN EACH DIMER, WITH TWO SITES PER DIMER AND FOUR PER TETRAMER.
Sequence detailsSINCE THE SEQUENCE FOR PDC FROM SACCHAROMYCES UVARUM IS NOT KNOWN, THE MODEL WAS BUILT ASSUMING THE ...SINCE THE SEQUENCE FOR PDC FROM SACCHAROMYCES UVARUM IS NOT KNOWN, THE MODEL WAS BUILT ASSUMING THE HOMOLOGOUS SACCHAROMYCES CEREVISIAE PDC1 SEQUENCE WAS APPROPRIATE. THE CEREVISIAE SEQUENCE INDEED FIT THE ELECTRON DENSITY EXTREMELY WELL, AND ONLY TWO DIFFERENCES ARE REFLECTED IN THE DEPOSITED COORDINATES: ARG 55 - ALA 55 AND VAL 538 - ILE 538. THE CEREVISIAE SEQUENCE USED WAS REPORTED EARLIER BY HOHMANN, EG "STRUCTURE AND EXPRESSION OF YEAST PYRUVATE DECARBOXYLASE STRUCTURAL GENES", HOHMANN, S. (1991) IN BIOCHEMISTRY AND PHYSIOLOGY OF THIAMIN DIPHOSPHATE ENZYMES" (BISSWANGER, H. & ULLRICH, J., EDS.) PP106 - 114, VCH PUBLISHERS, NEW YORK.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlpyruvate decarboxylase1drop
210 %(w/v)PEG80001dropprecipitant
30.02 Mcitric acid1dropor sodium citrate
40.002 Mthiamin diphosphate1drop
50.002 M1dropMgCl2
60.001 Mdithiothreitol1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 40681 / % possible obs: 92 % / Num. measured all: 192609 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.197 / Rfactor obs: 0.197 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 54 2 8316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å / σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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