CDC48 / YDL126C Overview
- Standard Name
- CDC48 1
- Systematic Name
- YDL126C
- SGD ID
- SGD:S000002284
- Feature Type
- ORF , Verified
- Description
- AAA ATPase with protein-unfoldase activity; subunit of polyUb-selective segregase complex involved in ERAD, INM-associated degradation (INMAD), mitotic spindle disassembly, macroautophagy, PMN, ribosome-associated degradation, ribophagy, homotypic ER membrane fusion, SCF complex disassembly, cell wall integrity, and telomerase regulation; mobilizes membrane-anchored transcription factors by regulated Ub/proteasome-dependent processing (RUP); human ortholog VCP complements a cdc48 mutant 2 3 4 5 6 7 8 9 10 11 12 13 14
- Name Description
- Cell Division Cycle 1
- 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.
- Summary
- Cdc48p is 835 amino acids long and undergoes various post-translational modifications including acetylation, phosphorylation, succinylation, sumoylation, and ubiquitinylation on 50 residues
- Length (a.a.)
- 835
- Mol. Weight (Da)
- 91954.8
- Isoelectric Point
- 4.56
- Median Abundance (molecules/cell)
- 29012 +/- 7816
- Half-life (hr)
- 9.4
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 CDC48 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
- ATPase, a component of several multiprotein ATPase complexes involved in the release of polyubiquitinated proteins; part of the ER-associated ubiquitin-dependent protein degradation system, stress-induced homeostatically regulated protein degradation (SHRED) pathway; also plays a role in mitotic spindle disassembly, autophagy, ER membrane fusion, retrograde protein transport; localized throughout the cell
View computational annotations
Molecular Function
- Manually Curated
- enables ATP hydrolysis activity (IDA)
- enables polyubiquitin modification-dependent protein binding (IDA)
- enables protein phosphatase regulator activity (IMP)
- enables ubiquitin binding (IDA)
Biological Process
- Manually Curated
- involved in cytoplasm protein quality control by the ubiquitin-proteasome system (IMP)
- involved in DNA replication termination (IDA)
- involved in endoplasmic reticulum membrane fusion (IMP)
- acts upstream of or within endosome to plasma membrane protein transport (IMP)
- involved in ERAD pathway (IMP)
- involved in macroautophagy (IMP)
- involved in mitochondria-associated ubiquitin-dependent protein catabolic process (IMP)
- involved in mitotic DNA replication termination (IMP)
- involved in mitotic spindle disassembly (IMP)
- involved in nonfunctional rRNA decay (IMP)
- involved in nuclear protein quality control by the ubiquitin-proteasome system (IMP)
- involved in piecemeal microautophagy of the nucleus (IMP)
- involved in positive regulation of mitochondrial fusion (IMP)
- involved in positive regulation of protein localization to nucleus (IMP)
- involved in proteasome-mediated ubiquitin-dependent protein catabolic process (IMP)
- involved in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (IGI, IMP)
- involved in protein-containing complex disassembly (IGI, IMP)
- involved in retrograde protein transport, ER to cytosol (IMP, IDA)
- involved in ribophagy (IMP)
- involved in ribosome-associated ubiquitin-dependent protein catabolic process (IMP, IDA)
- involved in SCF complex disassembly in response to cadmium stress (IMP)
- involved in sister chromatid biorientation (IMP)
- involved in stress-induced homeostatically regulated protein degradation pathway (IMP)
Cellular Component
- Manually Curated
- part of Cdc48p-Npl4p-Vms1p AAA ATPase complex (IDA)
- located in cytosol (IDA, HDA)
- part of Doa10p ubiquitin ligase complex (IDA)
- located in endoplasmic reticulum membrane (IDA)
- part of Hrd1p ubiquitin ligase ERAD-L complex (IDA)
- located in mating projection tip (HDA)
- located in mitochondrion (HDA)
- located in nucleus (HDA, IDA)
- part of replisome (IDA)
- part of RQC complex (IPI, IDA)
- part of VCP-NPL4-UFD1 AAA ATPase complex (IDA)
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
- Essential gene; conditional mutations cause cell cycle arrest, abnormal cell morphology, aggregation of mitochondria, elongated spindles that fail to disassemble, sensitivity to cell wall-affecting drugs and oxidative stress; overexpression leads to slow growth
Classical Genetics
- overexpression
- reduction of function
- repressible
- conditional
- autophagy: decreased
- cell cycle progression in G1 phase: delayed
- cell cycle progression in M phase: arrested
- cell cycle progression in metaphase: arrested
- cell cycle progression: abnormal
- cell cycle progression: arrested
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chromosome/plasmid maintenance: decreased
- cold sensitivity: increased
- heat sensitivity: increased
- nuclear import: absent
- nuclear position: abnormal
- protein/peptide accumulation: abnormal
- protein/peptide accumulation: increased
- protein/peptide distribution: abnormal
- protein/peptide distribution: increased duration
- protein/peptide modification: decreased
- protein/peptide modification: increased
- resistance to chemicals: decreased
- ribophagy: decreased
- silencing: decreased
- spindle morphology: abnormal
- telomere length: decreased
- toxin resistance: decreased
- vegetative growth: decreased
- activation
- null
- null
- overexpression
- repressible
- reduction of function
- conditional
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 CDC48 is homologous to human VCP, and has been used to study amyotrophic lateral sclerosis 14 (aka frontotemporal dementia and/or amyotrophic lateral sclerosis-6), Charcot-Marie-Tooth disease type 2Y, and inclusion body myopathy with Paget disease of bone and frontotemporal dementia
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.
- Summary
- Cdc48p nteracts physically with proteins involved in protein catabolism; CDC48 interacts genetically with genes involved in transcription
1624 total interactions for 949 unique genes
Physical Interactions
- Affinity Capture-MS: 277
- Affinity Capture-RNA: 6
- Affinity Capture-Western: 163
- Biochemical Activity: 2
- Co-crystal Structure: 1
- Co-localization: 2
- Co-purification: 5
- FRET: 1
- Protein-peptide: 2
- Proximity Label-MS: 4
- Reconstituted Complex: 54
- Two-hybrid: 37
Genetic Interactions
- Dosage Growth Defect: 2
- Dosage Lethality: 1
- Dosage Rescue: 36
- Negative Genetic: 739
- Phenotypic Enhancement: 8
- Phenotypic Suppression: 20
- Positive Genetic: 218
- Synthetic Growth Defect: 20
- Synthetic Lethality: 12
- Synthetic Rescue: 14
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.
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.
Summary Paragraph
A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.
Last Updated: 2024-05-23
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.