DID4 / YKL002W Overview


Standard Name
DID4 1
Systematic Name
YKL002W
SGD ID
SGD:S000001485
Aliases
VPS14 12 , GRD7 13 , REN1 2 , VPL2 14 , VPT14 15 , CHM2 16 , VPS2 15 17
Feature Type
ORF , Verified
Description
Class E Vps protein of the ESCRT-III complex; required for sorting of integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthesized vacuolar enzymes to the vacuole, involved in endocytosis 1 2 3 4
Name Description
Doa4-Independent Degradation 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
DID4 is on the left arm of chromosome XI very close to the centromere, between MRP17 mitochondrial ribosomal protein and MET14 adenylylsulfate kinase; coding sequence is 767 nucleotides long with an intron at 61..128, 5 silent SNPs, and 2 SNPs that cause amino acid polymorphisms at residues 204 (Pro/Ala) and 215 (Glu/Asp)
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
Did4p is 232 amino acids long, shorter-lived, and low in abundance; phosphorylated on 4 serines
Length (a.a.)
232
Mol. Weight (Da)
26286.1
Isoelectric Point
4.96
Median Abundance (molecules/cell)
2857 +/- 1299
Half-life (hr)
8.9

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 DID4 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
Subunit of ESCRT III complex involved in ATP export, intralumenal vesicle formation and protein retention in golgi apparatus; localizes to cytoplasm

View computational annotations

Molecular Function

Manually Curated

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
Non-essential gene; null mutant exhibits heat sensitivity, sensitivity to caffeine, Congo Red, and other chemicals, and defects in vacuolar protein targeting; in large-scale studies, null mutant has reduced competitive fitness in several different media, sensitivity to heat shock, desiccation, and osmotic stress, poor utilization of various nitrogen sources, and altered resistance to many chemicals
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
DID4 is homologous to human CHMP2B and has been used to study amyotrophic lateral sclerosis type 17, which is now called chromosome 3-linked 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
Did4p interacts physically with proteins involved in vesicle organization, translation, protein targeting, and RNA catabolism; DID4 interacts genetically with genes involved in transcription

362 total interactions for 235 unique genes

Physical Interactions

  • Affinity Capture-MS: 20
  • Affinity Capture-RNA: 8
  • Affinity Capture-Western: 32
  • Co-crystal Structure: 1
  • Co-localization: 1
  • Far Western: 1
  • FRET: 1
  • PCA: 6
  • Protein-peptide: 1
  • Reconstituted Complex: 4
  • Two-hybrid: 14

Genetic Interactions

  • Dosage Rescue: 1
  • Negative Genetic: 196
  • Phenotypic Enhancement: 6
  • Phenotypic Suppression: 2
  • Positive Genetic: 37
  • Synthetic Growth Defect: 20
  • Synthetic Haploinsufficiency: 1
  • Synthetic Lethality: 2
  • Synthetic Rescue: 8
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
DID4 promoter is bound by Fkh2p in response to starvation, and by Xbp2p in response to heat; DID4 transcription is regulated by Cad1p under oxidative stress
Regulators
5
Targets
0
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.


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: 2006-03-13

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
58
Additional
52
Reviews
35

Resources