1R30

The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme

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	d1r30a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Radical SAM enzymes	Biotin synthase	Biotin synthase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1r30b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Radical SAM enzymes	Biotin synthase	Biotin synthase	(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	SCOP2 Family	Biotin synthase	8027899	4000977	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Radical SAM enzymes	8040278	3000308	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Radical SAM enzymes	8040278	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	PF04055,PF06968	e1r30A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF06968	ECOD (1.6)
B	PF04055,PF06968	e1r30B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF06968	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

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	PF06968	Biotin and Thiamin Synthesis associated domain (BATS)	Biotin and Thiamin Synthesis associated domain	Biotin synthase (BioB), EC:2.8.1.6 , catalyses the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer [1]. Thiamin synthesis if a complex proces ...	Biotin synthase (BioB), EC:2.8.1.6 , catalyses the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer [1]. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this family) and form a heterodimer[2]. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers [1,2]. This domain therefore may be involved in co-factor binding or dimerisation (Finn, RD personal observation).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Biotin synthase	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding small molecule binding biotin synthase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding metal cluster binding small molecule binding biotin synthase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity 4 iron, 4 sulfur cluster binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	biotin metabolic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process vitamin biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process amide metabolic process water-soluble vitamin metabolic process biotin metabolic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process vitamin biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process amide metabolic process water-soluble vitamin metabolic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process amide biosynthetic process biotin biosynthetic process vitamin metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process monocarboxylic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007197	Radical SAM	Domain
A, B	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain	Domain
A, B	IPR002684	Biotin synthase/Biotin biosynthesis bifunctional protein BioAB	Family
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR010722	Biotin and thiamin synthesis-associated domain	Domain
A, B	IPR024177	Biotin synthase	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	biotin synthase M-CSA #767	Biotin synthase (BioB) is a member of the radical-SAM superfamily. It catalyses the insertion of an S atom between the C6 and C9 carbon atoms of dethiobiotin (DTB). BioB contains [4Fe-4S] clusters involved in the reduction and cleavage of S-adenosyl-L-methionine (AdoMet), generating methionine and a primary 5'-deoxyadenosyl radical responsible for dethiobiotin H-abstraction. i.e. BioB is involved in the activation of AdoMet in the biotin synthesis pathway and the incorporation of S atoms into DTB. An oxygen sensitive Fe/S cluster is bound to each polypeptide chain and is chelated by three catalytic Cys residues. The cluster provides electrons for AdoMet cleavage and can adopt both +1 and +2 redox states.	Defined by 7 residues: CYS:A-76 [auth A-53]CYS:A-80 [auth A-57]CYS:A-83 [auth A-60]CYS:A-120 [auth A-97]CYS:A-151 [auth A-128]CYS:A-211 [auth A-188]ARG:A-283 [auth A-260] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.8.1.6 (PDB Primary Data) Search M-CSA Motif + EC 2.8.1.6

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.