1W85

The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1w85a_	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	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
C	d1w85c_	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	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
E	d1w85e_	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	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G	d1w85g_	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	Pyruvate dehydrogenase E1-alpha, PdhA	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1w85b1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1w85b2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d1w85d1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d1w85d2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H	d1w85h1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H	d1w85h2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d1w85f1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d1w85f2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
I	d1w85i_	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	E3/E1 binding domain of dihydrolipoyl acetyltransferase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
J	d1w85j_	All alpha proteins	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	E3/E1 binding domain of dihydrolipoyl acetyltransferase	(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	SCOP2 Family	Branched-chain alpha-keto acid dehydrogenase PP module	8030947	4003592	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043326	3001790	SCOP2B (2022-06-29)
B	SCOP2 Family	Branched-chain alpha-keto acid dehydrogenase Pyr module	8030945	4003570	SCOP2 (2022-06-29)
B	SCOP2 Family	BCKDE1B C-terminal domain-like	8030946	4000496	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2 (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)
H	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TK C-terminal domain-like	8043325	3000424	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8043324	3001790	SCOP2B (2022-06-29)
I	SCOP2 Family	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8030952	4000730	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8043331	3001183	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)
A	E1_dh	e1w85A1	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	e1w85C1	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)
E	E1_dh	e1w85E1	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)
G	E1_dh	e1w85G1	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	e1w85B1	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	e1w85B2	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	e1w85D1	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	e1w85D2	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)
H	Transketolase_C	e1w85H1	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)
H	Transket_pyr	e1w85H2	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)
F	Transketolase_C	e1w85F1	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)
F	Transket_pyr	e1w85F2	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	E3_binding	e1w85I1	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	e1w85J1	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)
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)
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)
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)
H	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
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)
F	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
I	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF00676	Dehydrogenase E1 component (E1_dh)	Dehydrogenase E1 component	-	Family
B, D, F, 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, F, 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
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, E, G	PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT	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	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 cellular catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic 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 cellular catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic process small molecule catabolic process amino acid catabolic process	-
B, D, F, H	PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT	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	-	-
I, J	DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE	fatty acid binding organic acid binding binding ion binding organic cyclic compound binding anion binding lipid binding lipoic acid binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding acetyltransferase activity fatty acid binding organic acid binding binding ion binding organic cyclic compound binding anion binding lipid binding lipoic acid binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding 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, E, G	IPR017596	Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha	Family
A, C, E, G	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, C, E, G	IPR050771	Alpha-ketoacid dehydrogenase complex E1 component	Family
A, C, E, G	IPR001017	Dehydrogenase, E1 component	Domain
B, D, F, H	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
B, D, F, H	IPR051467	PDH_E1_beta_subunit	Unknown
B, D, F, H	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
B, D, F, H	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
B, D, F, H	IPR033248	Transketolase, C-terminal domain	Domain
I, J	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
I, J	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
I, J	IPR036625	E3-binding domain superfamily	Homologous Superfamily
I, J	IPR050743	2-oxoacid dehydrogenase family, E2 component	Family
I, J	IPR004167	Peripheral subunit-binding domain	Domain
I, J	IPR011053	Single hybrid motif	Homologous Superfamily
I, J	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
I, J	IPR000089	Biotin/lipoyl attachment	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
B, C	pyruvate dehydrogenase (acetyl-transferring) M-CSA #106	Pyruvate decarboxylase (E1) catalyzes the first two reactions of the four involved in oxidative decarboxylation of pyruvate by the pyruvate dehydrogenase (PDH) multienzyme complex. It requires thiamin diphosphate to bring about the decarboxylation of pyruvate, which is followed by the reductive acetylation of a lipoyl group covalently bound to the N(6) amino group of a lysine residue in the second catalytic component, a dihydrolipoyl acetyltransferase (E2). The lipoamide is covalently bound to dihydrolipoamide acetyltransferase (the second catalytic component of the Pyruvate Dehydrogenase Complex) forming (dihydrolipoyllysine-residue acetyltransferase) lipoyllysine [PMID:12795594]. The enzyme consists of two catalytic sites, each providing TDP (thiamine diphosphate) and magnesium as cofactors and each formed on the interface between the aplha and beta subunits [PMID:12651851].	Defined by 5 residues: GLU:B-59HIS:B-128ARG:C-267HIS:C-271TYR:C-281 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.2.4.1 (PDB Primary Data) Search M-CSA Motif + EC 1.2.4.1

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.