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LCB1 long-chain base1 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 829800, updated on 18-Sep-2024

Summary

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Official Symbol
LCB1
Official Full Name
long-chain base1
Primary source
TAIR:AT4G36480
Locus tag
AT4G36480
See related
Araport:AT4G36480
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
AP22.60; AP22_60; ATLCB1; EMB2779; EMBRYO DEFECTIVE 2779; FBR11; FUMONISIN B1 RESISTANT 11; long-chain base1
Summary
Encodes the LCB1 subunit of serine palmitoyltransferase. Together with the LCB2 subunit, forms a functional serine palmitoyltransferase complex, which catalyzes the first reaction of sphingolipid biosynthesis. Knockout of LCB1 was embryo lethal. Partial suppression of LCB1 expression led to smaller plants due to reduced cell expansion.
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Genomic context

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See LCB1 in Genome Data Viewer
Location:
chromosome: 4
Exon count:
13
Sequence:
Chromosome: 4; NC_003075.7 (17217909..17221625)

Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene S-adenosyl-L-methionine-dependent methyltransferases superfamily protein Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene SEC14-like 12 Neighboring gene ncRNA Neighboring gene uncharacterized protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Involvement of sphingoid bases in mediating reactive oxygen intermediate production and programmed cell death in Arabidopsis. Shi L, et al. Cell Res, 2007 Dec. PMID 18059378
  2. Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis. Teng C, et al. Plant Physiol, 2008 Mar. PMID 18218968, Free PMC Article
  3. Arabidopsis 56-amino acid serine palmitoyltransferase-interacting proteins stimulate sphingolipid synthesis, are essential, and affect mycotoxin sensitivity. Kimberlin AN, et al. Plant Cell, 2013 Nov. PMID 24214397, Free PMC Article
  4. ORM Expression Alters Sphingolipid Homeostasis and Differentially Affects Ceramide Synthase Activity. Kimberlin AN, et al. Plant Physiol, 2016 Oct. PMID 27506241, Free PMC Article
  5. The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase. Chen M, et al. Plant Cell, 2006 Dec. PMID 17194770, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. expression confined in microspores during microgametogenesis, suggesting that serine palmitoyltransferase-modulated programmed cell death plays an important role in the regulation of male gametophyte development
    Title: Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis.
  2. The predicted gene for Arabidopsis thaliana LCB1 encodes a genuine subunit of Serine palmitoyltransferase (SPT) that rescues the sphingolipid long-chain base auxotrophy of Saccharomyces cerevisiae SPT mutants when coexpressed with Arabidopsis LCB2.
    Title: The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase.
Submit: New GeneRIF Correction

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

NM_001036719.2
NM_119811.3

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables serine C-palmitoyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables serine C-palmitoyltransferase activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within embryo development ending in seed dormancy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within multidimensional cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of programmed cell death IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in chloroplast ISM
Inferred from Sequence Model
more info
  
located_in endoplasmic reticulum HDA PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
long-chain base1
NP_001031796.1
  • long-chain base1 (LCB1); FUNCTIONS IN: protein binding, serine C-palmitoyltransferase activity; INVOLVED IN: cell growth, sphingolipid biosynthetic process; LOCATED IN: endoplasmic reticulum; EXPRESSED IN: 20 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Pyridoxal phosphate-dependent transferase, major domain (InterPro:IPR015424), Aminotransferase, class I/classII (InterPro:IPR004839), Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (InterPro:IPR015421); BEST Arabidopsis thaliana protein match is: long chain base2 (TAIR:AT5G23670.2); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
NP_568005.1
  • long-chain base1 (LCB1); FUNCTIONS IN: protein binding, serine C-palmitoyltransferase activity; INVOLVED IN: cell growth, sphingolipid biosynthetic process; LOCATED IN: endoplasmic reticulum; EXPRESSED IN: 20 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Pyridoxal phosphate-dependent transferase, major domain (InterPro:IPR015424), Aminotransferase, class I/classII (InterPro:IPR004839), Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (InterPro:IPR015421); BEST Arabidopsis thaliana protein match is: long chain base2 (TAIR:AT5G23670.2); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_003075.7 Reference assembly

    Range
    17217909..17221625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001342410.1 → NP_001329288.1  long-chain base1 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A1P8B789
    Conserved Domains (1) summary
    cl18945
    Location:1 → 335
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  2. NM_119811.3 → NP_568005.1  long-chain base1 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_568005.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    B9DHA0, O23233, Q94IB8
    UniProtKB/TrEMBL
    A0A178UY56, A0A5S9Y010
    Conserved Domains (1) summary
    PLN02822
    Location:1 → 481
    PLN02822; serine palmitoyltransferase

  3. NM_001036719.2 → NP_001031796.1  long-chain base1 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_001031796.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    B9DHA0, O23233, Q94IB8
    UniProtKB/TrEMBL
    A0A178UY56, A0A5S9Y010
    Conserved Domains (1) summary
    PLN02822
    Location:1 → 481
    PLN02822; serine palmitoyltransferase
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q94IB8.1

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