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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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