2G28

E. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiamin Diphosphate Complex

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)
B	d2g28b1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	TK-like Pyr module	Pyruvate dehydrogenase E1 component, Pyr module	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2g28b2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	TK-like PP module	Pyruvate dehydrogenase E1 component, PP module	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2g28b3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Transketolase C-terminal domain-like	Pyruvate dehydrogenase E1 component, C-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2g28a1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	TK-like Pyr module	Pyruvate dehydrogenase E1 component, Pyr module	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2g28a2	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	TK-like PP module	Pyruvate dehydrogenase E1 component, PP module	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2g28a3	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Transketolase C-terminal domain-like	Pyruvate dehydrogenase E1 component, C-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041598	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041600	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8041601	3000424	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041598	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TK C-terminal domain-like	8041601	3000424	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041600	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)
B	Transketolase_C_1	e2g28B3	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C_1	ECOD (1.6)
B	Transketolase_N	e2g28B4	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: Transketolase_N	ECOD (1.6)
B	aceE	e2g28B1	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: aceE	ECOD (1.6)
A	Transketolase_C_1	e2g28A1	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: Transketolase_C_1	ECOD (1.6)
A	Transketolase_N	e2g28A2	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: Transketolase_N	ECOD (1.6)
A	aceE	e2g28A3	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: aceE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17831	Pyruvate dehydrogenase E1 component middle domain (PDH_E1_M)	Pyruvate dehydrogenase E1 component middle domain	This entry represents one of the thiamin diphosphate-binding domains found in pyruvate dehydrogenase E1 component [1].	Domain
A, B	PF00456	Transketolase, thiamine diphosphate binding domain (Transketolase_N)	Transketolase, thiamine diphosphate binding domain	This family includes transketolase enzymes EC:2.2.1.1. and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit Swiss:P37941 EC:1.2.4.4. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common ...	This family includes transketolase enzymes EC:2.2.1.1. and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit Swiss:P37941 EC:1.2.4.4. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.	Domain
A, B	PF22613	Transketolase-like TK C-terminal domain (Transketolase_C_1)	Transketolase-like TK C-terminal domain	This entry represents the C-terminal domain found in transketolase and transketolase-like enzymes [1-5], such as pyruvate dehydrogenase E1 component (OPD1) [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Pyruvate dehydrogenase E1 component	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity pyruvate dehydrogenase (acetyl-transferring) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity pyruvate dehydrogenase (acetyl-transferring) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors pyruvate dehydrogenase activity catalytic activity molecular adaptor activity vitamin binding thiamine pyrophosphate binding organic cyclic compound binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	pyruvate metabolic process catabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process pyruvate metabolic process catabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process pyruvate catabolic process	protein-containing complex catalytic complex oxidoreductase complex pyruvate dehydrogenase complex alpha-ketoacid dehydrogenase complex membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005474	Transketolase, N-terminal	Domain
A, B	IPR004660	Pyruvate dehydrogenase E1 component	Family
A, B	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
A, B	IPR051157	Pyruvate Dehydrogenase/Transketolase	Family
A, B	IPR035807	Pyruvate dehydrogenase E1 component, N-terminal	Domain
A, B	IPR041621	Pyruvate dehydrogenase E1 component, middle domain	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.