1YBE | pdb_00001ybe

Crystal Structure of a Nicotinate phosphoribosyltransferase

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)
B	d1ybeb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Nicotinate/Quinolinate PRTase C-terminal domain-like	Nicotinate phosphoribosyltransferase C-terminal domain-like	Nicotinate phosphoribosyltransferase, C-terminal domain	(Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
B	d1ybeb2	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	Nicotinate/Quinolinate PRTase N-terminal domain-like	Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like	Nicotinate phosphoribosyltransferase, N-terminal domain	(Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
A	d1ybea1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Nicotinate/Quinolinate PRTase C-terminal domain-like	Nicotinate phosphoribosyltransferase C-terminal domain-like	Nicotinate phosphoribosyltransferase, C-terminal domain	(Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
A	d1ybea2	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	Nicotinate/Quinolinate PRTase N-terminal domain-like	Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like	Nicotinate phosphoribosyltransferase, N-terminal domain	(Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase N-terminal domain-like	8044297	3000867	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase C-terminal domain-like	8044296	3000603	SCOP2B (2022-06-29)
A	SCOP2 Family	Monomeric nicotinate phosphoribosyltransferase C-terminal domain	8031918	4002556	SCOP2 (2022-06-29)
A	SCOP2 Family	Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like	8031919	4002550	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nicotinate/Quinolinate PRTase C-terminal domain-like	8044296	3000603	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nicotinate/Quinolinate PRTase N-terminal domain-like	8044297	3000867	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Ribosomal_L16	e1ybeB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Ribosomal_L16	ECOD (develop294)
B	DUF711	e1ybeB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (develop294)
A	NAPRTase_N	e1ybeA1	A: few secondary structure elements	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Nicotinate/Quinolinate PRTase N-terminal domain-like	F: NAPRTase_N	ECOD (develop294)
A	NAPRTase	e1ybeA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: Nicotinate/Quinolinate PRTase C-terminal domain-like	T: Nicotinate/Quinolinate PRTase C-terminal domain-like	F: NAPRTase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.140.10	Alpha Beta	Alpha-Beta Barrel	nicotinate phosphoribosyltransferase	nicotinate phosphoribosyltransferase	CATH (4.3.0)
A	3.20.140.10	Alpha Beta	Alpha-Beta Barrel	nicotinate phosphoribosyltransferase	nicotinate phosphoribosyltransferase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04095	Nicotinate phosphoribosyltransferase (NAPRTase) family (NAPRTase)	Nicotinate phosphoribosyltransferase (NAPRTase) family	-	Family
A, B	PF17767	Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain (NAPRTase_N)	Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain	Nicotinate phosphoribosyltransferase (EC:2.4.2.11) is the rate limiting enzyme that catalyses the first reaction in the NAD salvage synthesis. This is the N-terminal domain of the enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Nicotinate phosphoribosyltransferase	nicotinate phosphoribosyltransferase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	pyridine nucleotide salvage nucleotide biosynthetic process NAD+ biosynthetic process nucleobase-containing compound metabolic process nucleotide salvage metabolic compound salvage purine nucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleotide salvage phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide salvage nucleotide biosynthetic process NAD+ biosynthetic process nucleobase-containing compound metabolic process nucleotide salvage metabolic compound salvage purine nucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleotide salvage phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process purine-containing compound salvage NAD+ biosynthetic process via the salvage pathway pyridine-containing compound biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nicotinamide nucleotide biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine nucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040727	Nicotinate phosphoribosyltransferase, N-terminal domain	Domain
A, B	IPR007229	Nicotinate phosphoribosyltransferase family	Family
A, B	IPR041525	Nicotinate/nicotinamide phosphoribosyltransferase	Domain
A, B	IPR006406	Nicotinate phosphoribosyltransferase	Family
A, B	IPR036068	Nicotinate phosphoribosyltransferase-like, C-terminal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.