5WHY

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8106656	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Radical SAM enzymes	8106653	3000308	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8106656	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Radical SAM enzymes	8106653	3000308	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	F_UNCLASSIFIED	e5whyA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF04055,PF13186	e5whyA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF13186	ECOD (1.6)
B	F_UNCLASSIFIED	e5whyB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF04055,PF13186	e5whyB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF13186	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
A, B	PF13186	Iron-sulfur cluster-binding domain (SPASM)	Iron-sulfur cluster-binding domain	This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, Pfam:PF04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ...	This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, Pfam:PF04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.	Domain
A, B	PF13353	4Fe-4S single cluster domain (Fer4_12)	4Fe-4S single cluster domain	This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Radical SAM domain protein	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007197	Radical SAM	Domain
A, B	IPR023885	4Fe4S-binding SPASM domain	Domain
A, B	IPR000385	MoaA/NifB/PqqE, iron-sulphur binding, conserved site	Conserved Site
A, B	IPR047602	Sactionine bond-forming enzyme CteB-like, SPASM domain	Domain
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR024025	SCIFF radical SAM maturase	Family
A, B	IPR023867	Anaerobic sulphatase maturase, radical SAM	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.