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 Details

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.


Summary
CDC48 is located on the left arm of chromosome IV between replication origin ARS409.5 and HNT1 adenosine 5'-monophosphoramidase; coding sequence is 2508 nucleotides long with 23 SNPs, 22 of which are silent, and 1 that leads to an Asp/Glu amino acid polymorphism at residue 493
Protein Details

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. Click "YeastMine" to view all alleles in YeastMine.


View all CDC48 alleles in SGD search | YeastMine

Gene Ontology Details

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

Biological Process

Manually Curated

Cellular Component

Manually Curated

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 Details

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
activation
null
Disease Details

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 Details

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

1601 total interactions for 946 unique genes

Physical Interactions

  • Affinity Capture-MS: 272
  • Affinity Capture-RNA: 6
  • Affinity Capture-Western: 155
  • Biochemical Activity: 2
  • Co-crystal Structure: 1
  • Co-localization: 2
  • Co-purification: 5
  • FRET: 1
  • Protein-peptide: 2
  • Proximity Label-MS: 1
  • Reconstituted Complex: 48
  • Two-hybrid: 37

Genetic Interactions

  • Dosage Growth Defect: 2
  • Dosage Lethality: 1
  • Dosage Rescue: 35
  • Negative Genetic: 739
  • Phenotypic Enhancement: 8
  • Phenotypic Suppression: 20
  • Positive Genetic: 218
  • Synthetic Growth Defect: 20
  • Synthetic Lethality: 12
  • Synthetic Rescue: 14
Regulation Details

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.


Summary
Promoter bound by Tec1p, and by Gcn5p, Med2p, Rgr1p, Sua7p, Tfc7p, and Uga3p during response to heat; transcription regulated by Gcr1p and Sin4p; transcription regulated by Sfp1p in response to stress
Regulators
11
Targets
1
Expression Details

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 Details

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.


Primary
169
Additional
152
Reviews
135

Resources