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- PDB-1pvd: CRYSTAL STRUCTURE OF THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYR... -

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Basic information

Entry
Database: PDB / ID: 1pvd
TitleCRYSTAL STRUCTURE OF THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE FROM THE YEAST SACCHAROMYCES CEREVISIAE AT 2.3 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: 2.3 Å
AuthorsFurey, W. / Arjunan, P.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution.
Authors: Arjunan, P. / Umland, T. / Dyda, F. / Swaminathan, S. / Furey, W. / Sax, M. / Farrenkopf, B. / Gao, Y. / Zhang, D. / 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. / Farrenkopf, B. / Jordan, F.
#2: Journal: Biochemistry and Physiology of Thiamin Diphosphate Enzymes
Year: 1991
Title: Structure and Expression of Yeast Pyruvate Decarboxylase Structural Genes
Authors: Hohmann, S.
#3: 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
DepositionApr 20, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: 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 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3826
Polymers121,4822
Non-polymers8994
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-64 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.060, 74.750, 120.320
Angle α, β, γ (deg.)90.00, 116.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9115, -0.0493, -0.4084), (-0.0403, -0.9773, 0.2079), (-0.4094, 0.2059, 0.8888)
Vector: 1.8318, -1.4298, 0.4654)
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 (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. 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. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 2 .. 556 B 2 .. 556 1.282

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Components

#1: Protein PYRUVATE DECARBOXYLASE


Mass: 60741.148 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.: 439 / 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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
210 %(w/v)PEG1drop
30.01 Mcitric acid/sodium citrate buffer1drop
40.002 Mthiamin diphosphate1drop
50.002 M1dropMgCl2
60.001 Mdithiothreitol1drop
7PEG80001reservoir

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Data collection

ReflectionResolution: 2.3→40 Å / Num. obs: 46787 / % possible obs: 92.9 % / Observed criterion σ(F): 2
Reflection
*PLUS
% possible obs: 93 % / Num. measured all: 199754 / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→10 Å / σ(F): 2
Details: REFERENCE 1 DESCRIBES THE TRANSFORMATION TO THE MONOCLINIC FORM AND ROTATION FUNCTION RESULTS. (APPROPRIATE FOR BOTH SACCHAROMYCES UVARUM AND SACCHAROMYCES CEREVISIAE). REFERENCE 3 DESCRIBES ...Details: REFERENCE 1 DESCRIBES THE TRANSFORMATION TO THE MONOCLINIC FORM AND ROTATION FUNCTION RESULTS. (APPROPRIATE FOR BOTH SACCHAROMYCES UVARUM AND SACCHAROMYCES CEREVISIAE). REFERENCE 3 DESCRIBES THE TRICLINIC CRYSTALS OF THE RELATED SACCHAROMYCES UVARUM FORM.
RfactorNum. reflection% reflection
Rwork0.165 --
obs0.165 46196 92.8 %
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 54 439 8753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.1
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
Num. reflection obs: 46787
Solvent computation
*PLUS
Displacement parameters
*PLUS

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