PEP5 / YMR231W Overview
- Standard Name
- PEP5 1
- Systematic Name
- YMR231W
- SGD ID
- SGD:S000004844
- Aliases
- VPT11 8 , END1 9 , VAM1 10 , VPL9 11 , VPS11 8 11
- Feature Type
- ORF , Verified
- Description
- Histone E3 ligase, component of CORVET membrane tethering complex; peripheral vacuolar membrane protein required for protein trafficking and vacuole biogenesis; interacts with Pep7p; involved in ubiquitination and degradation of excess histones 2 3 4 6 7
- Name Description
- carboxyPEPtidase Y-deficient 5
- Comparative Info
-
Sequence
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.
Analyze Sequence
S288C only
BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation
S288C vs. other species
BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi
S288C vs. other strains
Protein
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.
- Length (a.a.)
- 1029
- Mol. Weight (Da)
- 117455.4
- Isoelectric Point
- 5.61
- Median Abundance (molecules/cell)
- 2031 +/- 353
- Half-life (hr)
- 7.3
Alleles
Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.
View all PEP5 alleles in SGD search
Gene Ontology
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.
- Summary
- E3 ubiquitin protein-ligase involved in the catabolism of histones; subunit of both the HOPS complex, which is involved in vacuolar fusion, and the CORVET membrane tethering complex, which is involved in vacuolar biogenesis and endosome to vacuole transport
View computational annotations
Molecular Function
- Manually Curated
- contributes to phosphatidylinositol binding (IDA)
- enables ubiquitin protein ligase activity (IDA)
- enables zinc ion binding (RCA)
Biological Process
- Manually Curated
- involved in Golgi to endosome transport (IGI)
- involved in histone catabolic process (IMP)
- involved in late endosome to vacuole transport (IGI)
- involved in regulation of SNARE complex assembly (IDA)
- involved in vacuole fusion, non-autophagic (IMP, IDA)
- involved in vesicle tethering (IDA)
Cellular Component
- Manually Curated
- part of CORVET complex (IDA)
- located in fungal-type vacuole membrane (IDA)
- part of HOPS complex (IPI)
Complex
Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.
Phenotype
Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.
- Summary
- PEP5/YMR231W is a non-essential gene; null mutants are viable but exhibit a range of phenotypic changes including absent autophagy and endocytosis, abnormal cellular and vacuolar morphology, decreased hydrostatic pressure resistance, decreased mating efficiency, decreased metal resistance, abnormal protein/peptide distribution, altered resistance to chemicals, decreased acid and alkaline pH resistance, decreased biofilm formation, abnormal chemical compound accumulation and excretion, abnormal colony appearance and increased sectoring, increased heat sensitivity, absent invasive growth, abnormal lipid particle morphology, decreased protein/peptide modification, decreased RNA accumulation, decreased toxin resistance, decreased utilization rates of carbon and nitrogen sources, and decreased vegetative growth rate. Reduction of function mutants exhibit decreased endocytosis, decreased hyperosmotic stress resistance, decreased pheromone-induced cell cycle arrest, abnormal protein/peptide accumulation, decreased shmoo formation, and abnormal or absent vacuolar morphology and transport. Conditional mutants display increased heat sensitivity.
Classical Genetics
- null
- reduction of function
- conditional
- null
- acid pH resistance: decreased
- alkaline pH resistance: decreased
- biofilm formation: decreased
- chemical compound accumulation: abnormal
- chemical compound excretion: increased
- colony appearance: abnormal
- colony sectoring: increased
- heat sensitivity: increased
- hydrostatic pressure resistance: decreased
- invasive growth: absent
- lipid particle morphology: abnormal
- protein/peptide distribution: abnormal
- protein/peptide modification: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- RNA accumulation: decreased
- toxin resistance: decreased
- utilization of carbon source: decreased rate
- utilization of nitrogen source: decreased rate
- vacuolar morphology: abnormal
- vegetative growth: decreased
- vegetative growth: decreased rate
- viable
Large-scale Survey
Disease
Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.
- Summary
- Yeast PEP5/VPS11 is homologous to human VPS11, and has been used to study Parkinson's disease risk and hypomyelinating leukodystrophy, an autosomal recessive neurological disease characterized by acquired microcephaly, delayed myelination, and severely delayed, or absent, psychomotor development that becomes apparent in the first months of life
Manually Curated
Interaction
Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.
230 total interactions for 96 unique genes
Physical Interactions
- Affinity Capture-MS: 44
- Affinity Capture-RNA: 4
- Affinity Capture-Western: 51
- Biochemical Activity: 2
- Co-localization: 1
- Co-purification: 6
- PCA: 2
- Proximity Label-MS: 2
- Reconstituted Complex: 17
- Two-hybrid: 29
Genetic Interactions
- Dosage Growth Defect: 1
- Negative Genetic: 3
- Phenotypic Enhancement: 6
- Phenotypic Suppression: 8
- Synthetic Growth Defect: 26
- Synthetic Lethality: 26
- Synthetic Rescue: 2
Regulation
The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.
- Regulators
- 2
- Targets
- 0
Expression
Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.
Literature
All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.