2VK1 | pdb_00002vk1

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2vk1d2	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d2vk1d1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2vk1c2	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2vk1c1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2vk1b2	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2vk1b1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2vk1a2	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	automated matches	automated matches	YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2vk1a1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	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)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044266	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044248	3001728	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044267	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8044248	3001728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044267	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044266	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044266	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)	8044267	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)	8044266	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8044267	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)
D	TPP_enzyme_M	e2vk1D1	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)
D	TPP_enzyme_C	e2vk1D3	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)
D	TPP_enzyme_N	e2vk1D2	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)
C	TPP_enzyme_M	e2vk1C1	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)
C	TPP_enzyme_C	e2vk1C3	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)
C	TPP_enzyme_N	e2vk1C2	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	e2vk1B1	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	e2vk1B3	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	e2vk1B2	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)
A	TPP_enzyme_M	e2vk1A1	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	e2vk1A3	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	e2vk1A2	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)
D	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
D	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
C	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
C	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, C, D	PF02775	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C)	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain		Domain
A, B, C, D	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, C, D	PYRUVATE DECARBOXYLASE ISOZYME 1	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 anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	catabolic process oxoacid 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 carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process catabolic process oxoacid 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 carboxylic acid catabolic process metabolic process cellular process small molecule metabolic 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 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 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 indole-containing compound metabolic process L-tryptophan metabolic process L-tryptophan catabolic process indole-containing compound catabolic process small molecule biosynthetic process amino acid catabolic process via Ehrlich pathway aromatic amino acid family catabolic process to alcohol via Ehrlich pathway biosynthetic process amino acid catabolic process to alcohol via Ehrlich pathway alcohol biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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, C, D	IPR012001	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain	Domain
A, B, C, D	IPR000399	TPP-binding enzyme, conserved site	Conserved Site
A, B, C, D	IPR047214	Pyruvate decarboxylase/indolepyruvate decarboxylase-like, PP-binding domain	Domain
A, B, C, D	IPR012000	Thiamine pyrophosphate enzyme, central domain	Domain
A, B, C, D	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C, D	IPR012110	Pyruvate decarboxylase/indolepyruvate decarboxylase-like	Family
A, B, C, D	IPR047213	Pyruvate decarboxylase/indolepyruvate decarboxylase-like, pyrimidine-binding domain	Domain
A, B, C, D	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	Domain

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.