1D0S | pdb_00001d0s

CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE : 5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH 5, 6-DIMETHYLBENZIMIDAZOLE

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	d1d0sa_	Alpha and beta proteins (a/b)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CobT-like	8042890	3000212	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	DBI_PRT	e1d0sA1	A: a/b three-layered sandwiches	X: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) (From Topology)	H: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) (From Topology)	T: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	F: DBI_PRT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1610.10	Mainly Alpha	Orthogonal Bundle	5,6-Dimethylbenzimidazole Phosphoribosyltransferase	Chain: A	CATH (4.3.0)
A	3.40.50.10210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02277	Phosphoribosyltransferase (DBI_PRT)	Phosphoribosyltransferase	This family of proteins represent the nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase (NN:DBI PRT) enzymes involved in dimethylbenzimidazole synthesis. This function is essential to de novo cobalamin (vitamin B12) production in ...	This family of proteins represent the nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase (NN:DBI PRT) enzymes involved in dimethylbenzimidazole synthesis. This function is essential to de novo cobalamin (vitamin B12) production in bacteria. Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity pentosyltransferase activity glycosyltransferase activity transferase activity catalytic activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process tetrapyrrole metabolic process small molecule biosynthetic process vitamin biosynthetic process vitamin metabolic process tetrapyrrole biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process water-soluble vitamin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023195	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal	Homologous Superfamily
A	IPR036087	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily	Homologous Superfamily
A	IPR003200	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase	Family
A	IPR017846	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase M-CSA #79	Nicotinate mononucleotide:5,6- dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) is crucial in the synthesis of alpha-ribose-5'-phosphate, a precursor to the lower ligand of colbamin. The biosynthesis of colbamin requires more than 25 committed enzymes, and the biosynthetic pathway has received much interest because of its complexity. Colbamin synthesis is also of interest in evolutionary biology because of its utilisation by early forms of bacteria and Archaea. The enzyme has also been shown to act on benzimidazole, and the clostridial enzyme acts on adenine to form 7-alpha-D-ribosyladenine 5'-phosphate.	Defined by 2 residues: GLU:A-174GLU:A-317 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.4.2.21 (PDB Primary Data) Search M-CSA Motif + EC 2.4.2.21

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.