6B58

FrdA-SdhE assembly intermediate

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)
D	d6b58d_	All alpha proteins	YgfY-like	YgfY-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d6b58b_	All alpha proteins	YgfY-like	YgfY-like	automated matches	automated matches	(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)
A	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056077	3000021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056076	3000054	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056076	3000054	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056077	3000021	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	PF02910	e6b58A1	A: alpha bundles	X: Spectrin repeat-like	H: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	F: PF02910	ECOD (1.6)
A	PF00890	e6b58A3	A: a+b complex topology	X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	H: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	F: PF00890	ECOD (1.6)
A	PF00890	e6b58A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF00890	ECOD (1.6)
C	PF02910	e6b58C2	A: alpha bundles	X: Spectrin repeat-like	H: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	F: PF02910	ECOD (1.6)
C	PF00890	e6b58C1	A: a+b complex topology	X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	H: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	F: PF00890	ECOD (1.6)
C	PF00890	e6b58C3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF00890	ECOD (1.6)
D	PF03937	e6b58D1	A: alpha arrays	X: YgfY-like (DUP399, Pfam03937) (From Topology)	H: YgfY-like (DUP399, Pfam03937) (From Topology)	T: YgfY-like (DUP399, Pfam03937)	F: PF03937	ECOD (1.6)
B	PF03937	e6b58B1	A: alpha arrays	X: YgfY-like (DUP399, Pfam03937) (From Topology)	H: YgfY-like (DUP399, Pfam03937) (From Topology)	T: YgfY-like (DUP399, Pfam03937)	F: PF03937	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.150.250	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	1.10.150.250	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF02910	Fumarate reductase flavoprotein C-term (Succ_DH_flav_C)	Fumarate reductase flavoprotein C-term	This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases.	Domain
A, C	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	-	Family
B, D	PF03937	Flavinator of succinate dehydrogenase (Sdh5)	Flavinator of succinate dehydrogenase	This family includes the highly conserved mitochondrial and bacterial proteins Sdh5/SDHAF2/SdhE. Both yeast and human Sdh5/SDHAF2 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron trans ...	This family includes the highly conserved mitochondrial and bacterial proteins Sdh5/SDHAF2/SdhE. Both yeast and human Sdh5/SDHAF2 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Mutational inactivation of Sdh5 confers tumor susceptibility in humans [1]. Bacterial homologues of Sdh5, termed SdhE, are functionally conserved being required for the flavinylation of SdhA and succinate dehydrogenase activity. Like Sdh5, SdhE interacts with SdhA. Furthermore, SdhE was characterised as a FAD co-factor chaperone that directly binds FAD to facilitate the flavinylation of SdhA. Phylogenetic analysis demonstrates that SdhE/Sdh5 proteins evolved only once in an ancestral alpha-proteobacteria prior to the evolution of the mitochondria and now remain in subsequent descendants including eukaryotic mitochondria and the alpha, beta and gamma proteobacteria [2]. This family was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true. The E. coli protein, YgfY also acts as the antitoxin to the membrane-bound toxin family Cpta, Pfam:PF13166, whose E. coli member YgfX, expressed from the same operon as YgfY [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Fumarate reductase flavoprotein subunit	oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding succinate dehydrogenase (quinone) activity electron transfer activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy anaerobic respiration fermentation organelle assembly cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly cellular component biogenesis cellular component organization bacterial-type flagellum organization organelle organization cellular component assembly cellular component organization or biogenesis cell projection assembly	respiratory chain complex protein-containing complex catalytic complex plasma membrane protein complex membrane plasma membrane plasma membrane respirasome membrane protein complex cellular anatomical entity cell periphery fumarate reductase complex plasma membrane respiratory chain complex II plasma membrane fumarate reductase complex respiratory chain complex II respiratory chain complex protein-containing complex catalytic complex plasma membrane protein complex membrane plasma membrane plasma membrane respirasome membrane protein complex cellular anatomical entity cell periphery fumarate reductase complex plasma membrane respiratory chain complex II plasma membrane fumarate reductase complex respiratory chain complex II respirasome intracellular anatomical structure cytoplasm cytosol
B, D	FAD assembly factor SdhE	-	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis respiratory chain complex II assembly succinate metabolic process organic substance metabolic process oxoacid metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis respiratory chain complex II assembly succinate metabolic process organic substance metabolic process oxoacid metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process organic acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
A, C	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
A, C	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A, C	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, C	IPR003953	FAD-dependent oxidoreductase 2, FAD binding domain	Domain
A, C	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A, C	IPR005884	Fumarate reductase, flavoprotein subunit	Family
A, C	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
A, C	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family
B, D	IPR036714	Flavinator of succinate dehydrogenase superfamily	Homologous Superfamily
B, D	IPR005631	Flavinator of succinate dehydrogenase	Family

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 R01GM133198.