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Q9LSZ9

- LCB2A_ARATH

UniProt

Q9LSZ9 - LCB2A_ARATH

Protein

Long chain base biosynthesis protein 2a

Gene

LCB2a

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 102 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      Previous versions | rss
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    Functioni

    Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1 constitutes the catalytic core. Involved in the regulation of the programmed cell death (PCD) signaling pathway. Plays an important role during male gametogenesis and embryogenesis.3 Publications

    Catalytic activityi

    Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.

    Cofactori

    Pyridoxal phosphate.By similarity

    Pathwayi

    GO - Molecular functioni

    1. protein binding Source: TAIR
    2. pyridoxal phosphate binding Source: InterPro
    3. serine C-palmitoyltransferase activity Source: TAIR

    GO - Biological processi

    1. apoptotic process Source: UniProtKB-KW
    2. photomorphogenesis Source: TAIR
    3. pollen development Source: TAIR
    4. regulation of programmed cell death Source: UniProtKB
    5. sphingosine biosynthetic process Source: TAIR

    Keywords - Molecular functioni

    Acyltransferase, Transferase

    Keywords - Biological processi

    Apoptosis, Lipid metabolism, Sphingolipid metabolism

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciARA:AT5G23670-MONOMER.
    ARA:GQT-1061-MONOMER.
    MetaCyc:AT5G23670-MONOMER.
    BRENDAi2.3.1.50. 302.
    ReactomeiREACT_190876. Sphingolipid de novo biosynthesis.
    UniPathwayiUPA00222.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Long chain base biosynthesis protein 2a (EC:2.3.1.50)
    Short name:
    AtLCB2a
    Alternative name(s):
    Long chain base biosynthesis protein 2
    Short name:
    AtLCB2
    Gene namesi
    Name:LCB2a
    Synonyms:LCB2
    Ordered Locus Names:At5g23670
    ORF Names:MQM1.6
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G23670.

    Subcellular locationi

    Endoplasmic reticulum membrane 1 Publication; Single-pass membrane protein 1 Publication

    GO - Cellular componenti

    1. endoplasmic reticulum Source: TAIR
    2. endoplasmic reticulum membrane Source: UniProtKB-SubCell
    3. integral component of membrane Source: UniProtKB-KW
    4. membrane Source: TAIR
    5. vacuole Source: TAIR

    Keywords - Cellular componenti

    Endoplasmic reticulum, Membrane

    Pathology & Biotechi

    Disruption phenotypei

    No visible phenotype. Lcb2a and lcb2b double mutant is not viable due to pollen lethality.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 489489Long chain base biosynthesis protein 2aPRO_0000419145Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei311 – 3111N6-(pyridoxal phosphate)lysineBy similarity

    Proteomic databases

    PRIDEiQ9LSZ9.

    Expressioni

    Tissue specificityi

    Ubiquitous. Detected in leaves, roots, stems, flowers and at a lower level in mature seeds.3 Publications

    Developmental stagei

    Detected at high levels in the petiole, sepals and petals in young flowers, but was not detected in the anthers during the early stages of pollen development.1 Publication

    Gene expression databases

    GenevestigatoriQ9LSZ9.

    Interactioni

    Subunit structurei

    Heterodimer with LCB1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (LCB2a or LCB2b).2 Publications

    Protein-protein interaction databases

    STRINGi3702.AT5G23670.2-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9LSZ9.
    SMRiQ9LSZ9. Positions 62-469.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei2 – 2221HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG0156.
    HOGENOMiHOG000206826.
    InParanoidiQ9LSZ9.
    KOiK00654.
    OMAiICLGHED.
    PhylomeDBiQ9LSZ9.

    Family and domain databases

    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProiIPR001917. Aminotrans_II_pyridoxalP_BS.
    IPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PfamiPF00155. Aminotran_1_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 1 hit.
    PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9LSZ9-1 [UniParc]FASTAAdd to Basket

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    MITIPYLTAV STYFSYGLLF AFGQLRDFFR RFIDWWFTSN LQGYAPICLG    50
    HEDFYIRRLY HRIQDCFERP ISSAPDAWFD VVERYSNDNN KTLKRTTKTS 100
    RCLNLGSYNY LGFGSFDEYC TPRVIESLKK FSASTCSSRV DAGTTSVHAE 150
    LEECVTRFVG KPAAVVFGMG YATNSAIIPV LIGKGGLIIS DSLNHSSIVN 200
    GARGSGATIR VFQHNTPSHL ERVLREQIAE GQPRTHRPWK KIIVVVEGIY 250
    SMEGEICHLP EVVAICKKYK AYVYLDEAHS IGAIGKTGKG ICELLGVDTA 300
    DVDVMMGTFT KSFGSCGGYI AGSKELIQYL KHQCPAHLYA TSIPTPSAQQ 350
    IISAIKVILG EDGSNRGAQK LARIRENSNF FRAELQKMGF EVLGDNDSPV 400
    MPIMLYNPAK IPAFSRECLR QKVAVVVVGF PATPLLLARA RICISASHSR 450
    EDLIRALKVI SKVGDLSGIK YFPAEPKKIE QSKNDIKLD 489
    Length:489
    Mass (Da):54,290
    Last modified:October 1, 2000 - v1
    Checksum:i00B396BB47D2E048
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti65 – 651D → N(PubMed:11171191)Curated
    Sequence conflicti65 – 651D → N in BAB03231. (PubMed:11726713)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB046384 mRNA. Translation: BAB03231.1.
    AB025633 Genomic DNA. Translation: BAA97234.1.
    CP002688 Genomic DNA. Translation: AED93196.1.
    CP002688 Genomic DNA. Translation: AED93197.1.
    AY050829 mRNA. Translation: AAK92764.1.
    AY133827 mRNA. Translation: AAM91761.1.
    AK316942 mRNA. Translation: BAH19645.1.
    RefSeqiNP_001031932.1. NM_001036855.1.
    NP_197756.1. NM_122272.3.
    UniGeneiAt.23395.
    At.49054.

    Genome annotation databases

    EnsemblPlantsiAT5G23670.1; AT5G23670.1; AT5G23670.
    AT5G23670.2; AT5G23670.2; AT5G23670.
    GeneIDi832432.
    KEGGiath:AT5G23670.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB046384 mRNA. Translation: BAB03231.1 .
    AB025633 Genomic DNA. Translation: BAA97234.1 .
    CP002688 Genomic DNA. Translation: AED93196.1 .
    CP002688 Genomic DNA. Translation: AED93197.1 .
    AY050829 mRNA. Translation: AAK92764.1 .
    AY133827 mRNA. Translation: AAM91761.1 .
    AK316942 mRNA. Translation: BAH19645.1 .
    RefSeqi NP_001031932.1. NM_001036855.1.
    NP_197756.1. NM_122272.3.
    UniGenei At.23395.
    At.49054.

    3D structure databases

    ProteinModelPortali Q9LSZ9.
    SMRi Q9LSZ9. Positions 62-469.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT5G23670.2-P.

    Proteomic databases

    PRIDEi Q9LSZ9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G23670.1 ; AT5G23670.1 ; AT5G23670 .
    AT5G23670.2 ; AT5G23670.2 ; AT5G23670 .
    GeneIDi 832432.
    KEGGi ath:AT5G23670.

    Organism-specific databases

    TAIRi AT5G23670.

    Phylogenomic databases

    eggNOGi COG0156.
    HOGENOMi HOG000206826.
    InParanoidi Q9LSZ9.
    KOi K00654.
    OMAi ICLGHED.
    PhylomeDBi Q9LSZ9.

    Enzyme and pathway databases

    UniPathwayi UPA00222 .
    BioCyci ARA:AT5G23670-MONOMER.
    ARA:GQT-1061-MONOMER.
    MetaCyc:AT5G23670-MONOMER.
    BRENDAi 2.3.1.50. 302.
    Reactomei REACT_190876. Sphingolipid de novo biosynthesis.

    Miscellaneous databases

    PROi Q9LSZ9.

    Gene expression databases

    Genevestigatori Q9LSZ9.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProi IPR001917. Aminotrans_II_pyridoxalP_BS.
    IPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view ]
    Pfami PF00155. Aminotran_1_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53383. SSF53383. 1 hit.
    PROSITEi PS00599. AA_TRANSFER_CLASS_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of a cDNA encoding serine palmitoyltransferase in Arabidopsis thaliana."
      Tamura K., Nishiura H., Mori J., Imai H.
      Biochem. Soc. Trans. 28:745-747(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    2. "Characterization of an Arabidopsis cDNA encoding a subunit of serine palmitoyltransferase, the initial enzyme in sphingolipid biosynthesis."
      Tamura K., Mitsuhashi N., Hara-Nishimura I., Imai H.
      Plant Cell Physiol. 42:1274-1281(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    3. "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones."
      Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S.
      DNA Res. 7:31-63(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    4. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    6. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
      Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
      DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 248-489.
      Strain: cv. Columbia.
      Tissue: Rosette leaf.
    7. "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., Han G., Dietrich C.R., Dunn T.M., Cahoon E.B.
      Plant Cell 18:3576-3593(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    8. "Loss-of-function mutations and inducible RNAi suppression of Arabidopsis LCB2 genes reveal the critical role of sphingolipids in gametophytic and sporophytic cell viability."
      Dietrich C.R., Han G., Chen M., Berg R.H., Dunn T.M., Cahoon E.B.
      Plant J. 54:284-298(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, SUBUNIT.
    9. "MPK6, sphinganine and the LCB2a gene from serine palmitoyltransferase are required in the signaling pathway that mediates cell death induced by long chain bases in Arabidopsis."
      Saucedo-Garcia M., Guevara-Garcia A., Gonzalez-Solis A., Cruz-Garcia F., Vazquez-Santana S., Markham J.E., Lozano-Rosas M.G., Dietrich C.R., Ramos-Vega M., Cahoon E.B., Gavilanes-Ruiz M.
      New Phytol. 191:943-957(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiLCB2A_ARATH
    AccessioniPrimary (citable) accession number: Q9LSZ9
    Secondary accession number(s): B9DFX8, Q9LRB4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2012
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 102 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The lcb2a-1 mutant is incapable of initiating programmed cell death (PCD) after induction by fumonisin B1 (FB1), a specific inhibitor of ceramide synthase.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3