3GRE | pdb_00003gre

Crystal structure of Saccharomyces cerevisiae Vps15 WD repeat domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ANAPC4_WD40_6	e3greA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: ANAPC4_WD40_6	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Serine/threonine-protein kinase VPS15	protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H2AS121 kinase activity histone modifying activity histone H2A kinase activity catalytic activity histone kinase activity AMP-activated protein kinase activity DNA-dependent protein kinase activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H2AS121 kinase activity histone modifying activity histone H2A kinase activity catalytic activity histone kinase activity AMP-activated protein kinase activity DNA-dependent protein kinase activity histone H3T45 kinase activity histone H3 kinase activity eukaryotic translation initiation factor 2alpha kinase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding histone H3T6 kinase activity histone H3T3 kinase activity histone H2BS14 kinase activity histone H2B kinase activity histone H3S57 kinase activity Rho-dependent protein serine/threonine kinase activity histone H2AT120 kinase activity protein binding ubiquitin binding ubiquitin-like protein binding histone H2AXS139 kinase activity histone H2AX kinase activity histone H4S1 kinase activity histone H4 kinase activity protein serine kinase activity histone H3T11 kinase activity histone H3S28 kinase activity 3-phosphoinositide-dependent protein kinase activity histone H2BS36 kinase activity histone H2AS1 kinase activity ribosomal protein S6 kinase activity histone H3S10 kinase activity	catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism maintenance of protein location protein localization cellular localization protein localization to Golgi apparatus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism maintenance of protein location protein localization cellular localization protein localization to Golgi apparatus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle protein retention in Golgi apparatus late endosome to vacuole transport transport establishment of localization in cell vacuolar transport intracellular transport establishment of localization vesicle-mediated transport phosphatidylinositol metabolic process glycerophospholipid biosynthetic process glycerophospholipid metabolic process lipid biosynthetic process primary metabolic process phosphatidylinositol phosphate biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process phospholipid metabolic process biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process autophagy of peroxisome macroautophagy pexophagy cellular component organization organelle organization vacuole organization organelle inheritance vacuole inheritance cellular component organization or biogenesis establishment of protein localization nitrogen compound transport protein targeting establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport protein targeting to vacuole intracellular protein transport transcription elongation by RNA polymerase II regulation of cellular process positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cellular response to potassium ion starvation cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation	nucleus-vacuole junction organelle membrane contact site cellular anatomical structure organelle phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane membrane protein complex transferase complex phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups phosphatidylinositol 3-kinase complex, class III extrinsic component of membrane nucleus-vacuole junction organelle membrane contact site cellular anatomical structure organelle phosphatidylinositol 3-kinase complex, class III, type II protein-containing complex catalytic complex membrane membrane protein complex transferase complex phosphatidylinositol 3-kinase complex transferase complex, transferring phosphorus-containing groups phosphatidylinositol 3-kinase complex, class III extrinsic component of membrane membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cytoplasm organelle membrane endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle mitochondrion vacuole-isolation membrane contact site phagophore assembly site membrane phagophore assembly site vacuolar membrane storage vacuole lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane fungal-type vacuole membrane phosphatidylinositol 3-kinase complex, class III, type I late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR000719	Protein kinase domain	Domain
A	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A	IPR021133	HEAT, type 2	Repeat
A	IPR011989	Armadillo-like helical	Homologous Superfamily
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR055231	VPS15-like, helical domain	Domain
A	IPR001680	WD40 repeat	Repeat
A	IPR045162	Serine/threonine-protein kinase Vps15-like	Family
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

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.