1VLP | pdb_00001vlp

Crystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from saccharomyces cerevisiae at 1.75 A resolution

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	d1vlpd2	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1vlpd1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1vlpd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1vlpc2	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1vlpc1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1vlpc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1vlpb2	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1vlpb1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1vlpa2	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1vlpa1	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	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1vlpa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase N-terminal domain-like	8041494	3000867	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase C-terminal domain-like	8041495	3000603	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase C-terminal domain-like	8041495	3000603	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase N-terminal domain-like	8041494	3000867	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase C-terminal domain-like	8041495	3000603	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nicotinate/Quinolinate PRTase N-terminal domain-like	8041494	3000867	SCOP2B (2022-06-29)
A	SCOP2 Family	Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like	8029115	4002550	SCOP2 (2022-06-29)
A	SCOP2 Family	Monomeric nicotinate phosphoribosyltransferase C-terminal domain	8029116	4002556	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nicotinate/Quinolinate PRTase N-terminal domain-like	8041494	3000867	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nicotinate/Quinolinate PRTase C-terminal domain-like	8041495	3000603	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)
D		e1vlpD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
D		e1vlpD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
C		e1vlpC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
C		e1vlpC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
B		e1vlpB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B		e1vlpB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
A		e1vlpA1	A: alpha/beta-Hammerhead/Barrel-sandwich hybrid	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: Nicotinate/Quinolinate PRTase N-terminal domain-like	T: NAPRTase_N	F:	ECOD (20:10:01)
A		e1vlpA2	A: TIM beta/alpha-barrel	X: Nicotinate/Quinolinate PRTase C-terminal domain-like	H: Nicotinate/Quinolinate PRTase C-terminal domain-like	T: NAPRTase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.140.10	Alpha Beta	Alpha-Beta Barrel	nicotinate phosphoribosyltransferase	nicotinate phosphoribosyltransferase	CATH (4.3.0)
C	3.20.140.10	Alpha Beta	Alpha-Beta Barrel	nicotinate phosphoribosyltransferase	nicotinate phosphoribosyltransferase	CATH (4.3.0)
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, C, D	PF04095	Nicotinate phosphoribosyltransferase (NAPRTase) family (NAPRTase)	Nicotinate phosphoribosyltransferase (NAPRTase) family	-	Family
A, B, C, D	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, C, D	nicotinate phosphoribosyltransferase	nicotinate phosphoribosyltransferase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity transferase activity	subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process pyridine nucleotide salvage nucleotide biosynthetic process nicotinate nucleotide biosynthetic process nucleotide salvage metabolic compound salvage nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process pyridine-containing compound biosynthetic process primary metabolic process nicotinate nucleotide salvage nucleobase-containing compound biosynthetic process nucleotide metabolic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation NAD+ biosynthetic process purine nucleotide metabolic process purine-containing compound biosynthetic process purine nucleotide salvage NAD+ metabolic process nicotinamide nucleotide metabolic process purine-containing compound salvage NAD+ biosynthetic process via the salvage pathway purine-containing compound metabolic process nicotinamide nucleotide biosynthetic process purine nucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR040727	Nicotinate phosphoribosyltransferase, N-terminal domain	Domain
A, B, C, D	IPR007229	Nicotinate phosphoribosyltransferase family	Family
A, B, C, D	IPR041525	Nicotinate/nicotinamide phosphoribosyltransferase	Domain
A, B, C, D	IPR006406	Nicotinate phosphoribosyltransferase	Family
A, B, C, D	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.