1OVM | pdb_00001ovm

Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae

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	d1ovmd1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Pyruvate oxidase and decarboxylase, middle domain	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
D	d1ovmd2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase Pyr module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
D	d1ovmd3	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase PP module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
C	d1ovmc1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Pyruvate oxidase and decarboxylase, middle domain	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
C	d1ovmc2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase Pyr module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
C	d1ovmc3	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase PP module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
B	d1ovmb1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Pyruvate oxidase and decarboxylase, middle domain	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
B	d1ovmb2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase Pyr module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
B	d1ovmb3	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase PP module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
A	d1ovma1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Pyruvate oxidase and decarboxylase, middle domain	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
A	d1ovma2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase Pyr module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	SCOPe (2.08)
A	d1ovma3	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate oxidase and decarboxylase PP module	Indole-3-pyruvate decarboxylase	(Enterobacter cloacae ) [TaxId: 550 ],	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)	8034394	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8034390	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8034388	3001728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8034394	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8034390	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8034388	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8034388	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8034394	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8034390	3001790	SCOP2B (2022-06-29)
A	SCOP2 Family	Pyruvate oxidase and decarboxylase, middle domain	8022008	4003891	SCOP2 (2022-06-29)
A	SCOP2 Family	Pyruvate oxidase and decarboxylase Pyr module	8022010	4003552	SCOP2 (2022-06-29)
A	SCOP2 Family	Pyruvate oxidase and decarboxylase PP module	8022014	4003580	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DHS-like NAD/FAD-binding domain	8034388	3001728	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8034390	3001790	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8034394	3001790	SCOP2 (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	e1ovmD1	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	e1ovmD3	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	e1ovmD2	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	e1ovmC1	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	e1ovmC3	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	e1ovmC2	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	e1ovmB1	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	e1ovmB3	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	e1ovmB2	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	e1ovmA1	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	e1ovmA3	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	e1ovmA2	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	Indole-3-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 indolepyruvate decarboxylase activity vitamin binding thiamine pyrophosphate binding 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 indolepyruvate decarboxylase activity vitamin binding thiamine pyrophosphate binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	catabolic process aromatic amino acid metabolic process oxoacid metabolic process small molecule biosynthetic process aromatic amino acid family catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process alcohol metabolic process organic acid catabolic process organic acid metabolic process amino acid catabolic process via Ehrlich pathway aromatic amino acid family catabolic process to alcohol via Ehrlich pathway biosynthetic process carboxylic acid catabolic process catabolic process aromatic amino acid metabolic process oxoacid metabolic process small molecule biosynthetic process aromatic amino acid family catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process alcohol metabolic process organic acid catabolic process organic acid metabolic process amino acid catabolic process via Ehrlich pathway aromatic amino acid family catabolic process to alcohol via Ehrlich pathway biosynthetic process carboxylic acid catabolic process amino acid catabolic process to alcohol via Ehrlich pathway alcohol biosynthetic process small molecule metabolic process metabolic process cellular process small molecule catabolic process amino acid catabolic process auxin metabolic process regulation of hormone levels auxin biosynthetic process biological regulation regulation of biological quality hormone biosynthetic process hormone metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	IPR017764	Indole-3-pyruvate decarboxylase, Enterobacteriaceae	Family
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.