DED1 / YOR204W Overview
- Standard Name
- DED1 1
- Systematic Name
- YOR204W
- SGD ID
- SGD:S000005730
- Aliases
- SPP81 10
- Feature Type
- ORF , Verified
- Description
- ATP-dependent DEAD-box RNA helicase with strand-annealing activity; promotes eIF4F-dependent 48S translation preinitiation complex (PIC) assembly, stimulating recruitment of mRNAs with long, structured 5'-UTRs; cooperates with Dbp1p in PIC attachment and scanning; ATPase activity stimulated by mRNA cap-associated factor binding; directly binds eIF4G; role in spliceosomal complex disassembly; mutation in human homolog DBY associated with male infertility; human homolog DDX3X complements the null 2 3 4 5 6 7 8 9
- Name Description
- Defines Essential Domain 1
- Paralog
- DBP1
- 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.
- Summary
- DED1/YOR204W is located on the near the middle of the right arm of chromsome XV between HIS3 imidazoleglycerol-phosphate dehydratase and GEP3 mitochondrial ribosome small subunit biogenesis protein; coding sequence is 1815 nucleotides long with a 4-aa inframe insertion in strain SK1 and 10 SNPs, 4 of which cause amino acid polymorphisms; DED1 has a paralog, DBP1, that arose from the whole genome duplication
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
- Ded1p is 604 amino acids long, slightly shorter-lived, high in abundance; contains disordered regions in both termini; methylated on 4 arginines, acetylated on K92 and K164, succinylated on K246 and K386, ubiquitinylated on 3 lysines, phosphorylated on 33 residues
- Length (a.a.)
- 604
- Mol. Weight (Da)
- 65554.7
- Isoelectric Point
- 7.98
- Median Abundance (molecules/cell)
- 25034 +/- 5043
- Half-life (hr)
- 9.1
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 DED1 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
- Bifunctional enzyme with both RNA strand-annealing and ATP-dependent RNA helicase activities; translation initiation factor involved in assembly of the translational preinitiation complex and disassembly of the spliceosomal complex; binds G-quadruplex (G4) nucleic acids and destabilizes G4RNA structures; localizes to the nucleus, cytoplasm, and cytoplasmic stress granule
View computational annotations
Molecular Function
- Manually Curated
- enables eukaryotic initiation factor 4G binding (IPI)
- enables G-quadruplex DNA binding (IDA)
- enables G-quadruplex RNA binding (IDA)
- enables mRNA binding (HDA, IDA)
- enables RNA helicase activity (IDA, IMP)
- enables RNA strand annealing activity (IDA)
Biological Process
- Manually Curated
- involved in positive regulation of formation of translation preinitiation complex (IDA, IMP)
- involved in spliceosomal complex disassembly (IDA)
- involved in translational initiation (IMP)
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 alleles confer cold sensitivity and slow growth even at permissive temperature; in a large-scale study, mutant exhibits MMS sensitivity
Classical Genetics
- overexpression
- conditional
- null
- overexpression
- 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 DED1 is homologous to human DDX3X, and has been used to study mutations associated with pediatric medulloblastoma
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
- Ded1p interacts physically with proteins involved in rRNA processing; DED1 interacts genetically with genes involved in transcription; the ded1 null mutant is inviable, the null mutant of paralog dbp1 is viable, the ded1 dbp1 double mutant shows decreased growth
2287 total interactions for 1895 unique genes
Physical Interactions
- Affinity Capture-MS: 216
- Affinity Capture-RNA: 16
- Affinity Capture-Western: 23
- Biochemical Activity: 3
- Co-fractionation: 9
- Co-purification: 2
- PCA: 12
- Protein-RNA: 22
- Proximity Label-MS: 6
- Reconstituted Complex: 24
- Two-hybrid: 1
Genetic Interactions
- Dosage Growth Defect: 3
- Dosage Lethality: 1
- Dosage Rescue: 19
- Negative Genetic: 1060
- Phenotypic Enhancement: 1
- Phenotypic Suppression: 5
- Positive Genetic: 840
- Synthetic Growth Defect: 9
- Synthetic Lethality: 10
- Synthetic Rescue: 5
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
- DED1 transcription is upregulated by Atg1p in response to nitrogen starvation
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.