LCB1 / YMR296C Overview


Standard Name
LCB1 1
Systematic Name
YMR296C
SGD ID
SGD:S000004911
Aliases
END8 , TSC2
Feature Type
ORF , Verified
Description
Component of serine palmitoyltransferase; responsible along with Lcb2p for the first committed step in sphingolipid synthesis, which is the condensation of serine with palmitoyl-CoA to form 3-ketosphinganine 1 2
Name Description
Long-Chain Base 1 3
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
LCB1 is located on the right arm of chromsome XIII near the telomere between YMR295C ribosome-associated protein and PRC1 vacuolar carboxypeptidase Y; coding sequence is 1677 nucleotides long with 13 SNPs, one of which leads to a Leu/Met amino acid polymorphism at residue 72
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
Lcb1p is 558 amino acids long, longer lived, and moderate in abundance; phosphorylated on 3 residues, ubiquitinylated on 2 lysines
Length (a.a.)
558
Mol. Weight (Da)
62198.6
Isoelectric Point
6.1
Median Abundance (molecules/cell)
9391 +/- 2462
Half-life (hr)
11.3

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 LCB1 alleles in SGD search

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
Serine palmitoyltransferase subunit involved in biosynthesis of sphingolipids; localized to the SPOTS complex in the endoplasmic reticulum

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.


Pathways


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; repression results in depletion of sphingoid long-chain bases, defects in endocytosis and shmoo formation, increased sensitivity to heat and oxidative stress
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 LCB1 is homologous to human SPTLC1 and has been used to study hereditary sensory and autonomic neuropathy type 1A and amyotrophic lateral sclerosis type 27
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
Lcb1p interacts physically with proteins involved in lipid metabolism; LCB1 interacts genetically with genes involved in mitosis

831 total interactions for 655 unique genes

Physical Interactions

  • Affinity Capture-MS: 30
  • Affinity Capture-RNA: 5
  • Affinity Capture-Western: 22
  • Co-purification: 9
  • PCA: 5
  • Protein-RNA: 1
  • Proximity Label-MS: 1
  • Reconstituted Complex: 1

Genetic Interactions

  • Dosage Growth Defect: 2
  • Dosage Rescue: 5
  • Negative Genetic: 609
  • Phenotypic Enhancement: 4
  • Phenotypic Suppression: 9
  • Positive Genetic: 98
  • Synthetic Growth Defect: 6
  • Synthetic Lethality: 6
  • Synthetic Rescue: 18
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
LCB1 promoter is bound by Reb1p, Rpd3p, and Stp1p in response to heat; LCB1 transcription is regulated by Sfp1p in response to stress
Regulators
8
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: 2007-10-05

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
49
Additional
52
Reviews
52

Resources