4CYF | pdb_00004cyf

The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Peptidase_M99_C	e4cyfB1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)
A	Peptidase_M99_C	e4cyfA1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.60.110.10	Alpha Beta	4-Layer Sandwich	Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase	Carbon-nitrogen hydrolase	CATH (4.3.0)
A	3.60.110.10	Alpha Beta	4-Layer Sandwich	Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase	Carbon-nitrogen hydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF19018	Vanin C-terminal domain (Vanin_C)	Vanin C-terminal domain	This domain is found at the C terminus of Vanin 1 and related proteins [1].	Domain
A, B	PF00795	Carbon-nitrogen hydrolase (CN_hydrolase)	Carbon-nitrogen hydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PANTETHEINASE	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides pantetheine hydrolase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process purine-containing compound catabolic process coenzyme A catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound catabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process purine-containing compound catabolic process coenzyme A catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound catabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process phosphorus metabolic process coenzyme A metabolic process chronic inflammatory response response to stimulus defense response response to stress inflammatory response acute inflammatory response biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus cell adhesion cell-cell adhesion cellular response to stimulus positive regulation of cell communication intrinsic apoptotic signaling pathway in response to oxidative stress regulation of cellular process positive regulation of signal transduction regulation of oxidative stress-induced intrinsic apoptotic signaling pathway signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction signal transduction intrinsic apoptotic signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation positive regulation of intracellular signal transduction cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway positive regulation of signaling response to oxidative stress multicellular organismal process regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development T cell differentiation in thymus positive regulation of developmental process multicellular organism development positive regulation of cell activation positive regulation of T cell differentiation in thymus T cell activation cell differentiation anatomical structure development positive regulation of leukocyte activation T cell differentiation regulation of immune system process positive regulation of immune system process developmental process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process leukocyte differentiation cellular developmental process regulation of developmental process cell development positive regulation of leukocyte cell-cell adhesion regulation of T cell differentiation in thymus lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of multicellular organismal process regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation pantothenate metabolic process oxoacid metabolic process modified amino acid metabolic process carboxylic acid metabolic process monocarboxylic acid metabolic process organic acid metabolic process	cellular anatomical structure membrane side of membrane extracellular region membrane-bounded organelle intracellular anatomical structure intracellular vesicle lytic vacuole endomembrane system intracellular organelle bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle cellular anatomical structure membrane side of membrane extracellular region membrane-bounded organelle intracellular anatomical structure intracellular vesicle lytic vacuole endomembrane system intracellular organelle bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle lysosome vacuolar membrane azurophil granule vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane organelle lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane cytoplasm organelle membrane secretory granule membrane cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR043957	Vanin, C-terminal	Domain
A, B	IPR012101	Biotinidase-like, eukaryotic	Family
A, B	IPR040154	Biotinidase/VNN family	Family
A, B	IPR003010	Carbon-nitrogen hydrolase	Domain
A, B	IPR036526	Carbon-nitrogen hydrolase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O95497	psoriasis Dyslipidemias inflammatory bowel disease ulcerative colitis atopic eczema esophageal adenocarcinoma lung carcinoma nephrosclerosis pancreatic intraductal papillary-mucinous neoplasm pustulosis palmaris et plantaris Crohn disease malignant mesothelioma osteosarcoma tuberculosis dermatitis, atopic psoriasis Dyslipidemias inflammatory bowel disease ulcerative colitis atopic eczema esophageal adenocarcinoma lung carcinoma nephrosclerosis pancreatic intraductal papillary-mucinous neoplasm pustulosis palmaris et plantaris Crohn disease malignant mesothelioma osteosarcoma tuberculosis dermatitis, atopic interstitial cystitis malignant pancreatic neoplasm ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.

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