ATG5 / YPL149W Overview


Standard Name
ATG5 1
Systematic Name
YPL149W
SGD ID
SGD:S000006070
Aliases
APG5 2
Feature Type
ORF , Verified
Description
Conserved protein involved in autophagy and the Cvt pathway; undergoes conjugation with Atg12p to form a complex involved in Atg8p lipidation; Atg5p-Atg12p conjugate enhances E2 activity of Atg3 by rearranging its catalytic site, also forms a complex with Atg16p; the Atg5-Atg12/Atg16 complex binds to membranes and is essential for autophagosome formation; also involved in methionine restriction extension of chronological lifespan in an autophagy-dependent manner 2 3 4 5 6 7 8
Name Description
AuTophaGy related 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
ATG5 is located on the left arm of chromosome XVI between YPL150W kinase and PPT2 phosphopantetheine:protein transferase; coding sequence is 885 nucleotides long with 10 SNPs, 6 of which cause amino acid polymorphisms
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
Atg5p is 294 amino acids long, extremely low in abundance
Length (a.a.)
294
Mol. Weight (Da)
33563.3
Isoelectric Point
8.77
Median Abundance (molecules/cell)
648 +/- 356

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 ATG5 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
Contributes to Atg8 ligase activity (conjugates Atg8p to phosphatidylethanolamine, PE); subunit of the Atg12-Atg5-Atg16 complex; involved in macroautophagy, cytoplasm-to-vacuole targeting (CVT) pathway, late nucleophagy, piecemeal microautophagy of nucleus, protein lipidation and mitochondrion degradation; localizes to the pre-autophagosomal structure (PAS)

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; reduction of function mutant is defective for autophagy and the CVT pathway; null mutant is unable to undergo both late nucleophagy and pexophagy, and displays reduced mitophagy and micronucleophagy; null mutant displays decreased viability during nitrogen starvation and abnormal nuclear morphology; null mutant displays a reduction in in the C-terminal modification of Atg8p and its localization to the pre-autophagosomal structure; null mutant has a reduction in chronological lifespan, and decreased resistance to desiccation and zinc treatment; homozygous diploid null mutant has a severe respiratory growth defect and is unable to sporulate; heterozygous diploid null is haploinsufficient
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 ATG5 is homologous to human ATG5, and has been used to study autosomal recessive spinocerebellar ataxia 25
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
Atg5p interacts physically with proteins involved in vacuole organization and protein targeting; ATG5 interacts genetically with genes involved in protein targeting

228 total interactions for 168 unique genes

Physical Interactions

  • Affinity Capture-MS: 10
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 8
  • Biochemical Activity: 3
  • Co-crystal Structure: 3
  • Co-fractionation: 2
  • Co-localization: 2
  • Co-purification: 2
  • PCA: 2
  • Reconstituted Complex: 16
  • Two-hybrid: 10

Genetic Interactions

  • Negative Genetic: 129
  • Phenotypic Enhancement: 3
  • Phenotypic Suppression: 7
  • Positive Genetic: 24
  • Synthetic Haploinsufficiency: 1
  • Synthetic Lethality: 2
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
ATG5 promoter is bound by Rgr1p in response to heat
Regulators
2
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: 2008-04-25

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
82
Additional
77
Reviews
143

Resources