4HDR | pdb_00004hdr

Crystal Structure of ArsAB in Complex 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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4hdrd_	Alpha and beta proteins (a/b)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	automated matches	automated matches	(Sporomusa ovata ) [TaxId: 2378 ],	SCOPe (2.08)
B	d4hdrb_	Alpha and beta proteins (a/b)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	automated matches	automated matches	(Sporomusa ovata ) [TaxId: 2378 ],	SCOPe (2.08)
C	d4hdrc_	Alpha and beta proteins (a/b)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	automated matches	automated matches	(Sporomusa ovata ) [TaxId: 2378 ],	SCOPe (2.08)
A	d4hdra_	Alpha and beta proteins (a/b)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	automated matches	automated matches	(Sporomusa ovata ) [TaxId: 2378 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	CobT-like	8084419	3000212	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CobT-like	8084419	3000212	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CobT-like	8084417	3000212	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CobT-like	8084417	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)
D	DBI_PRT	e4hdrD1	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)
B	DBI_PRT	e4hdrB1	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)
C	DBI_PRT	e4hdrC1	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)
A	DBI_PRT	e4hdrA1	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)
D	1.10.1610.10	Mainly Alpha	Orthogonal Bundle	5,6-Dimethylbenzimidazole Phosphoribosyltransferase	Chain: A	CATH (4.2.0)
D	3.40.50.10210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain	CATH (4.2.0)
B	1.10.1610.10	Mainly Alpha	Orthogonal Bundle	5,6-Dimethylbenzimidazole Phosphoribosyltransferase	Chain: A	CATH (4.2.0)
B	3.40.50.10210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain	CATH (4.2.0)
C	1.10.1610.10	Mainly Alpha	Orthogonal Bundle	5,6-Dimethylbenzimidazole Phosphoribosyltransferase	Chain: A	CATH (4.2.0)
C	3.40.50.10210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain	CATH (4.2.0)
A	1.10.1610.10	Mainly Alpha	Orthogonal Bundle	5,6-Dimethylbenzimidazole Phosphoribosyltransferase	Chain: A	CATH (4.2.0)
A	3.40.50.10210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
B, D	ArsB	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity pentosyltransferase activity glycosyltransferase activity transferase activity catalytic activity	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	-
A, C	ArsA	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity pentosyltransferase activity glycosyltransferase activity transferase activity catalytic activity	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR023195	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal	Homologous Superfamily
B, D	IPR036087	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily	Homologous Superfamily
B, D	IPR003200	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase	Family
A, C	IPR023195	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal	Homologous Superfamily
A, C	IPR036087	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily	Homologous Superfamily
A, C	IPR003200	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase	Family
A, C	IPR017846	Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.