3EY9

Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TPP_enzyme_M	e3ey9A1	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	e3ey9A3	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	e3ey9A2	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	e3ey9B6	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	e3ey9B5	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	e3ey9B4	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 dehydrogenase [cytochrome]	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding lipid binding flavin adenine dinucleotide binding nucleoside phosphate binding anion binding nucleotide binding heterocyclic compound binding quinone binding ubiquinone binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding lipid binding flavin adenine dinucleotide binding nucleoside phosphate binding anion binding nucleotide binding heterocyclic compound binding quinone binding ubiquinone binding oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, with a quinone or similar compound as acceptor oxidoreductase activity, acting on the aldehyde or oxo group of donors pyruvate dehydrogenase (quinone) activity catalytic activity vitamin binding thiamine pyrophosphate binding quaternary ammonium group binding sulfur compound binding identical protein binding protein binding	pyruvate metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process catabolic process organic acid catabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule catabolic process pyruvate metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process catabolic process organic acid catabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule catabolic process pyruvate catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex

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	IPR047210	Pyruvate oxidase POXB-like, pyrimidine-binding domain	Domain
A, B	IPR012000	Thiamine pyrophosphate enzyme, central domain	Domain
A, B	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B	IPR047212	Pyruvate oxidase POXB-like, PP-binding domain	Domain
A, B	IPR044261	Pyruvate dehydrogenase [ubiquinone]	Family
A, B	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding	Domain
A, B	IPR047211	Pyruvate oxidase/Pyruvate dehydrogenase [ubiquinone]-like	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A, B	pyruvate dehydrogenase (cytochrome) M-CSA #275	Catalyses the formation of acetate and carbon dioxide from pyruvate with the concomittant reduction of ubiquinone. This protein requires thiamine phosphate and FAD for activity. The bacterial enzyme is located on the inner surface of the cytoplasmic membrane and coupled to the respiratory chain via ubiquinone. It does not accept menaquinone as an acceptor. In Escherichia coli this is the primary complex responsible for aerobic growth, pyruvate oxidase (MACiE:274) acts as a backup system.	Defined by 5 residues: VAL:A-380PHE:A-465GLU:B-50PHE:B-112GLN:B-113 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.2.2.2 (PDB Primary Data) Search M-CSA Motif + EC 1.2.2.2 EC: 1.2.5.1 (UniProt) Search M-CSA Motif + EC 1.2.5.1

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.