Annotations: 4QOY

Novel binding motif and new flexibility revealed by structural analysis of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase sub-complex from the escherichia coli 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)
F	d4qoyf_	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	(Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)
E	d4qoye_	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	(Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076213	3001183	SCOP2B (2022-06-29)
E	SCOP2 Family	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076212	4000730	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8076213	3001183	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	TK C-terminal domain-like	8041601	3000424	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041600	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041598	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041598	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TK C-terminal domain-like	8041601	3000424	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041600	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041600	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041598	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	Thiamin diphosphate-binding fold (THDP-binding)	8041600	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TK C-terminal domain-like	8041601	3000424	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)
F		e4qoyF1	A: alpha arrays	X: DP domain	H: DP domain	T: DP domain	F:	ECOD (v295.2)
E		e4qoyE1	A: alpha arrays	X: DP domain	H: DP domain	T: DP domain	F:	ECOD (v295.2)
D	A2M_BRD	e4qoyD1	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: A2M_BRD	ECOD (v295.2)
C	A2M_BRD	e4qoyC1	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: A2M_BRD	ECOD (v295.2)
B	A2M_BRD	e4qoyB1	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: A2M_BRD	ECOD (v295.2)
A	NAD_binding_1	e4qoyA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: NAD_binding_1	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	CATH (4.3.0)
E	4.10.320.10	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase	E3-binding domain	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 (utative)
D	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
C	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (utative)
C	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (utative)
B	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (utative)
A	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	PF02817	e3 binding domain (E3_binding)	e3 binding domain	-	Family
A, B, C, D	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, C, D	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, C, D	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
E, F	Pyruvate dehydrogenase (Dihydrolipoyltransacetylase component)	fatty acid binding organic acid binding binding ion 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 fatty acid binding organic acid binding binding ion 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 catalytic activity	aerobic respiration cellular respiration energy derivation by oxidation of organic compounds oxoacid metabolic process acetyl-CoA metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process sulfur compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process aerobic respiration cellular respiration energy derivation by oxidation of organic compounds oxoacid metabolic process acetyl-CoA metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process sulfur compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process pyruvate metabolic process carboxylic acid metabolic process pyruvate decarboxylation to acetyl-CoA primary metabolic process generation of precursor metabolites and energy nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process monocarboxylic acid metabolic process	protein-containing complex catalytic complex oxidoreductase complex transferase complex pyruvate dehydrogenase complex acetyltransferase complex alpha-ketoacid dehydrogenase complex cellular anatomical structure intracellular anatomical structure cytoplasm
A, B, C, D	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 catalytic activity molecular adaptor activity vitamin binding thiamine pyrophosphate binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding	pyruvate metabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic 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 transferase complex pyruvate dehydrogenase complex acetyltransferase complex alpha-ketoacid dehydrogenase complex cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
E, F	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
E, F	IPR006256	Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex	Family
E, F	IPR036625	E3-binding domain superfamily	Homologous Superfamily
E, F	IPR050743	2-oxoacid dehydrogenase family, E2 component	Family
E, F	IPR004167	Peripheral subunit-binding domain	Domain
E, F	IPR011053	Single hybrid motif	Homologous Superfamily
E, F	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
E, F	IPR000089	Biotin/lipoyl attachment	Domain
A, B, C, D	IPR005474	Transketolase, N-terminal	Domain
A, B, C, D	IPR004660	Pyruvate dehydrogenase E1 component	Family
A, B, C, D	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C, D	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
A, B, C, D	IPR051157	Pyruvate Dehydrogenase/Transketolase	Family
A, B, C, D	IPR060495	Pyruvate dehydrogenase E1 component, N-terminal domain	Domain
A, B, C, D	IPR035807	Pyruvate dehydrogenase E1 component, N-terminal	Domain
A, B, C, D	IPR041621	Pyruvate dehydrogenase E1 component, middle domain	Domain
A, B, C, D	IPR055152	Transketolase-like, C-terminal domain	Domain

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.