1PVD

CRYSTAL STRUCTURE OF THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE FROM THE YEAST SACCHAROMYCES CEREVISIAE AT 2.3 ANGSTROMS RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1pvda1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Pyruvate oxidase and decarboxylase, middle domain	Pyruvate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1pvda2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase Pyr module	Pyruvate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1pvda3	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase PP module	Pyruvate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1pvdb1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Pyruvate oxidase and decarboxylase, middle domain	Pyruvate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1pvdb2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase Pyr module	Pyruvate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1pvdb3	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase PP module	Pyruvate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044266	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044248	3001728	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044267	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044267	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044248	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044266	3001790	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TPP_enzyme_M	e1pvdA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M	ECOD (1.6)
A	TPP_enzyme_C	e1pvdA3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
A	TPP_enzyme_N	e1pvdA2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)
B	TPP_enzyme_M	e1pvdB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: TPP_enzyme_M	ECOD (1.6)
B	TPP_enzyme_C	e1pvdB3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_C	ECOD (1.6)
B	TPP_enzyme_N	e1pvdB2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: TPP_enzyme_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
B	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00205	Thiamine pyrophosphate enzyme, central domain (TPP_enzyme_M)	Thiamine pyrophosphate enzyme, central domain	The central domain of TPP enzymes contains a 2-fold Rossman fold.	Domain
A, B	PF02775	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C)	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain	-	Domain
A, B	PF02776	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (TPP_enzyme_N)	Thiamine pyrophosphate enzyme, N-terminal TPP binding domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PYRUVATE DECARBOXYLASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyruvate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity branched-chain-2-oxoacid decarboxylase activity phenylpyruvate decarboxylase activity indolepyruvate decarboxylase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyruvate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity branched-chain-2-oxoacid decarboxylase activity phenylpyruvate decarboxylase activity indolepyruvate decarboxylase activity vitamin binding thiamine pyrophosphate binding organic cyclic compound binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	catabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process catabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic process small molecule catabolic process amino acid catabolic process aromatic amino acid family catabolic process alpha-amino acid metabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process L-phenylalanine catabolic process aromatic amino acid metabolic process L-amino acid catabolic process L-amino acid metabolic process L-phenylalanine metabolic process proteinogenic amino acid metabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process monosaccharide metabolic process carbohydrate metabolic process energy derivation by oxidation of organic compounds organic hydroxy compound metabolic process alcohol metabolic process hexose metabolic process generation of precursor metabolites and energy ethanol metabolic process fermentation glycolytic fermentation glycolytic fermentation to ethanol primary alcohol metabolic process glucose metabolic process amino acid catabolic process via Ehrlich pathway aromatic amino acid family catabolic process to alcohol via Ehrlich pathway small molecule biosynthetic process biosynthetic process organic hydroxy compound biosynthetic process amino acid catabolic process to alcohol via Ehrlich pathway alcohol biosynthetic process pyruvate metabolic process monocarboxylic acid metabolic process indole-containing compound metabolic process indolalkylamine metabolic process amine metabolic process indole-containing compound catabolic process tryptophan catabolic process biogenic amine metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012001	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain	Domain
A, B	IPR000399	TPP-binding enzyme, conserved site	Conserved Site
A, B	IPR047214	Pyruvate decarboxylase/indolepyruvate decarboxylase-like, PP-binding domain	Domain
A, B	IPR012000	Thiamine pyrophosphate enzyme, central domain	Domain
A, B	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B	IPR012110	Pyruvate decarboxylase/indolepyruvate decarboxylase-like	Family
A, B	IPR047213	Pyruvate decarboxylase/indolepyruvate decarboxylase-like, pyrimidine-binding domain	Domain
A, B	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	pyruvate decarboxylase M-CSA #215	pyruvate decarboxylase isoenzyme 1 (PDC1) is the major isoform of pyruvate decarboxylase and is implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. PDC1 is a thiamine diphosphate-dependent enzyme. It also requires Mg²⁺ for activity, however the magnesium is involved in anchoring the cofactor rather than directly involved in catalysis.	Defined by 9 residues: GLY:A-412 [auth A-413]ASP:A-443 [auth A-444]ASN:A-470 [auth A-471]GLY:A-472 [auth A-473]GLU:A-476 [auth A-477]ASP:B-27 [auth B-28]GLU:B-50 [auth B-51]HIS:B-113 [auth B-114]HIS:B-114 [auth B-115] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.1.1 (PDB Primary Data) Search M-CSA Motif + EC 4.1.1.1 EC: 4.1.1.74 (UniProt) Search M-CSA Motif + EC 4.1.1.74 EC: 4.1.1.72 (UniProt) Search M-CSA Motif + EC 4.1.1.72 EC: 4.1.1.43 (UniProt) Search M-CSA Motif + EC 4.1.1.43 EC: 4.1.1 (UniProt) Search M-CSA Motif + EC 4.1.1

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.