1DBS

MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE OF DETHIOBIOTIN SYNTHETASE

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)
A	d1dbsa_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nitrogenase iron protein-like	Dethiobiotin synthetase	(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	Simibi-like P-loop NTPases	8017784	3002018	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	AAA_26	e1dbsA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_26	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01656	CobQ/CobB/MinD/ParA nucleotide binding domain (CbiA)	CobQ/CobB/MinD/ParA nucleotide binding domain	This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA Swiss:P29946 and CbiP Swiss:Q05597 from S.typhimurium [4], and CobQ Swiss:Q52686 from R. capsulatus [3]. These amidases catalyse amidations to various side chai ...	This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA Swiss:P29946 and CbiP Swiss:Q05597 from S.typhimurium [4], and CobQ Swiss:Q52686 from R. capsulatus [3]. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [4]. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DETHIOBIOTIN SYNTHETASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding dethiobiotin synthase activity catalytic activity cyclo-ligase activity ligase activity, forming carbon-nitrogen bonds ligase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process biotin metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process vitamin biosynthetic process amide biosynthetic process organic acid biosynthetic process organic acid metabolic process biotin biosynthetic process carboxylic acid biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process biotin metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process vitamin biosynthetic process amide biosynthetic process organic acid biosynthetic process organic acid metabolic process biotin biosynthetic process carboxylic acid biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process amide metabolic process monocarboxylic acid metabolic process water-soluble vitamin metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004472	Dethiobiotin synthase BioD	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.