3DUF

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme 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)
A	d3dufa_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
C	d3dufc_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F [auth E]	d3dufe_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H [auth G]	d3dufg_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d3dufb1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d3dufb2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d3dufd1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d3dufd2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G [auth F]	d3duff1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G [auth F]	d3duff2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
I [auth H]	d3dufh1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
I [auth H]	d3dufh2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
E [auth I]	d3dufi_	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
J	d3dufj_	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	automated matches	automated matches	( ) [TaxId: ], (Geobacillus stearothermophilus ) [TaxId: 1422 ],	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)	8043326	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8043331	3001183	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	E1_dh	e3dufA1	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: E1_dh	ECOD (1.6)
C	E1_dh	e3dufC1	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: E1_dh	ECOD (1.6)
F [auth E]	E1_dh	e3dufE1	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: E1_dh	ECOD (1.6)
H [auth G]	E1_dh	e3dufG1	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: E1_dh	ECOD (1.6)
B	Transketolase_C	e3dufB3	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	ECOD (1.6)
B	Transket_pyr	e3dufB4	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: Transket_pyr	ECOD (1.6)
D	Transketolase_C	e3dufD3	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	ECOD (1.6)
D	Transket_pyr	e3dufD4	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: Transket_pyr	ECOD (1.6)
G [auth F]	Transketolase_C	e3dufF3	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	ECOD (1.6)
G [auth F]	Transket_pyr	e3dufF4	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: Transket_pyr	ECOD (1.6)
I [auth H]	Transketolase_C	e3dufH3	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	ECOD (1.6)
I [auth H]	Transket_pyr	e3dufH4	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: Transket_pyr	ECOD (1.6)
E [auth I]	E3_binding	e3dufI1	A: alpha arrays	X: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	H: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	T: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	F: E3_binding	ECOD (1.6)
J	E3_binding	e3dufJ1	A: alpha arrays	X: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	H: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex (From Topology)	T: Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	F: E3_binding	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)
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)
F [auth E]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
H [auth G]	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	3.40.50.970	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)
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	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
G [auth F]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
G [auth F]	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
I [auth H]	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
I [auth H]	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, C, F [auth E], H [auth G]	PF00676	Dehydrogenase E1 component (E1_dh)	Dehydrogenase E1 component	-	Family
B, D, G [auth F], I [auth H]	PF02779	Transketolase, pyrimidine binding domain (Transket_pyr)	Transketolase, pyrimidine binding domain	This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.	Domain
B, D, G [auth F], I [auth H]	PF02780	Transketolase, C-terminal domain (Transketolase_C)	Transketolase, C-terminal domain	The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site [2].	Domain
E [auth I], J	PF02817	e3 binding domain (E3_binding)	e3 binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, F [auth E], H [auth G]	Pyruvate dehydrogenase E1 component subunit alpha	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	-	-
B, D, G [auth F], I [auth H]	Pyruvate dehydrogenase E1 component subunit beta	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	-	-
E [auth I], J	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex	acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity dihydrolipoyllysine-residue acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity S-acetyltransferase activity S-acyltransferase activity catalytic activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, F [auth E], H [auth G]	IPR017596	Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha	Family
A, C, F [auth E], H [auth G]	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, C, F [auth E], H [auth G]	IPR050771	Alpha-ketoacid dehydrogenase complex E1 component	Family
A, C, F [auth E], H [auth G]	IPR001017	Dehydrogenase, E1 component	Domain
B, D, G [auth F], I [auth H]	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
B, D, G [auth F], I [auth H]	IPR051467	PDH_E1_beta_subunit	Unknown
B, D, G [auth F], I [auth H]	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
B, D, G [auth F], I [auth H]	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
B, D, G [auth F], I [auth H]	IPR033248	Transketolase, C-terminal domain	Domain
E [auth I], J	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
E [auth I], J	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
E [auth I], J	IPR036625	E3-binding domain superfamily	Homologous Superfamily
E [auth I], J	IPR050743	2-oxoacid dehydrogenase family, E2 component	Family
E [auth I], J	IPR004167	Peripheral subunit-binding domain	Domain
E [auth I], J	IPR011053	Single hybrid motif	Homologous Superfamily
E [auth I], J	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
E [auth I], J	IPR000089	Biotin/lipoyl attachment	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.