3V8E | pdb_00003v8e

Crystal structure of the yeast nicotinamidase Pnc1p bound to the inhibitor nicotinaldehyde

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	Isochorismatase-like hydrolases	8065860	3001778	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Isochorismatase-like hydrolases	8065860	3001778	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Isochorismatase-like hydrolases	8065860	3001778	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Isochorismatase-like hydrolases	8065860	3001778	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Isochorismatase-like hydrolases	8065860	3001778	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Isochorismatase-like hydrolases	8065860	3001778	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Isochorismatase-like hydrolases	8065860	3001778	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)
G	Vinculin	e3v8eG2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Vinculin	ECOD (v294.1)
F	ABC_tran	e3v8eF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
E	ABC_tran	e3v8eE1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
D	ABC_tran	e3v8eD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
C	ABC_tran	e3v8eC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
B	ABC_tran	e3v8eB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)
A	I-set	e3v8eA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: I-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	3.40.50.850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Isochorismatase-like	CATH (4.3.0)
F	3.40.50.850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Isochorismatase-like	CATH (4.3.0)
E	3.40.50.850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Isochorismatase-like	CATH (4.3.0)
D	3.40.50.850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Isochorismatase-like	CATH (4.3.0)
C	3.40.50.850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Isochorismatase-like	CATH (4.3.0)
B	3.40.50.850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Isochorismatase-like	CATH (4.3.0)
A	3.40.50.850	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Isochorismatase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	PF00857	Isochorismatase domain (Isochorismatase)	Isochorismatase domain	This is a domain found in hydrolase enzymes. This domain is responsible for the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate. It shows a typical helix-sheet-helix sandwich structural architecture, with ...	This is a domain found in hydrolase enzymes. This domain is responsible for the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate. It shows a typical helix-sheet-helix sandwich structural architecture, with a central beta--sheet made of six parallel strands, three alpha -helices on one side and two on the other [3,4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G	Nicotinamidase	amidase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides nicotinamidase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	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 regulation of DNA amplification regulation of DNA biosynthetic process regulation of primary metabolic process nucleic acid biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA amplification regulation of nucleobase-containing compound metabolic process DNA amplification DNA metabolic process nucleic acid metabolic process negative regulation of DNA metabolic process DNA biosynthetic process negative regulation of DNA biosynthetic process regulation of DNA metabolic process nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle peroxisome microbody cytoplasm intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle peroxisome microbody cytoplasm intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR000868	Isochorismatase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR052347	Isochorismatase Family Nicotinamidases	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR036380	Isochorismatase-like superfamily	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.