IDH1 / YNL037C Overview
- Standard Name
- IDH1 1
- Systematic Name
- YNL037C
- SGD ID
- SGD:S000004982
- Feature Type
- ORF , Verified
- Description
- Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase; complex catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle 2
- Name Description
- Isocitrate DeHydrogenase 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
- Idh1p is 360 amino acids long, long-lived, moderate in abundance; acetylated on 4 lysines, succinylated on 14 lysines, phosphorylated on 9 residues
- Length (a.a.)
- 360
- Mol. Weight (Da)
- 39328.5
- Isoelectric Point
- 9.54
- Median Abundance (molecules/cell)
- 12930 +/- 5858
- Half-life (hr)
- 15.8
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 IDH1 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
- Subunit of the mitochondrial NAD(+)-dependent isocitrate dehydrogenase complex, which catalyzes the oxidative decarboxylation of isocitrate to form 2-oxoglutarate; involved in glutamate biosynthesis and the tricarboxylic acid cycle; localizes to the mitochondrial matrix and nucleoid
View computational annotations
Molecular Function
- Manually Curated
- contributes to isocitrate dehydrogenase (NAD+) activity (IDA)
Biological Process
- Manually Curated
- involved in glutamate biosynthetic process (TAS)
- involved in isocitrate metabolic process (IDA)
- involved in tricarboxylic acid cycle (TAS)
Cellular Component
- Manually Curated
- part of isocitrate dehydrogenase complex (NAD+) (IDA)
- located in mitochondrial matrix (IDA)
- located in mitochondrial nucleoid (IDA)
- located in mitochondrion (HDA)
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.
Pathways
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; the null mutant exhibits a wide range of phenotypes includubg abnormal actin cytoskeleton morphology and decreased biofilm formation, indicating alterations in cell structure and adhesion properties. Mutants demonstrate poor chromosome and plasmid maintenance, as evidenced by large-scale survey assays. Chronological lifespan is diminished, and mutant strains show reduced competitive fitness during growth. The heterozygous diploid null is haploinsufficient. Mitochondrial genome maintenance is compromised in idh1 mutants, especially with specific mutations like A119R affecting isocitrate binding. The replicative lifespan is prolonged in these mutants, indicating a relationship between IDH1 function and cellular aging. While resistance to various chemicals is primarily decreased, there are instances of increased resistance to specific compounds. Mutant strains exhibit decreased respiratory growth rates and lower resistance to starvation. Moreover, they show absent or significantly reduced utilization of carbon sources, hampering metabolic flexibility. Nitrogen source utilization is also impaired, alongside overall decreased vegetative growth rates.
Classical Genetics
- unspecified
- null
- reduction of function
- null
- biofilm formation: decreased
- chromosome/plasmid maintenance: abnormal
- chronological lifespan: decreased
- competitive fitness: decreased
- haploinsufficient
- hyperosmotic stress resistance: decreased
- innate thermotolerance: increased
- metal resistance: increased
- protein/peptide accumulation: increased
- replicative lifespan: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: decreased rate
- starvation resistance: decreased
- stress resistance: increased
- toxin resistance: increased
- utilization of nitrogen source: decreased rate
- 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 IDH1 is homologous to human IDH3A, and has been used to study severe encephalopathy in infancy
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.
- Summary
- Idh1p interacts physically with proteins involved in rRNA processing; IDH1 interacts genetically with genes involved in transcription
447 total interactions for 312 unique genes
Physical Interactions
- Affinity Capture-MS: 84
- Affinity Capture-RNA: 5
- Affinity Capture-Western: 4
- Co-crystal Structure: 2
- Co-purification: 2
- Cross-Linking-MS (XL-MS): 3
- PCA: 1
- Proximity Label-MS: 2
- Reconstituted Complex: 2
- Two-hybrid: 3
Genetic Interactions
- Dosage Growth Defect: 1
- Dosage Rescue: 2
- Negative Genetic: 257
- Phenotypic Enhancement: 6
- Phenotypic Suppression: 4
- Positive Genetic: 51
- Synthetic Growth Defect: 11
- Synthetic Lethality: 4
- Synthetic Rescue: 3
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
- The expression of IDH1/YNL037C is regulated by a network of transcription factors that modulate its activity based on cellular conditions. Positive regulators include Usv1p and Znf1p. Transcription factors Bur6p and Sua7p play roles in mediating the cellular response to heat. Several other transcription factors bind the IDH1 promoter such as Abf1p, Cbf1p, Fkh1p, Met32p, Met4p, Pho2p, Rox1p, and Rrg3p. IDH1 transcription is negatively regulated by Msn2p/Msn4p.
- Regulators
- 17
- 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.
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: 2024-11-08
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.