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Q9M304

- LCB2B_ARATH

UniProt

Q9M304 - LCB2B_ARATH

Protein

Long chain base biosynthesis protein 2b

Gene

LCB2b

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 99 (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. Plays an important role during male gametogenesis and embryogenesis.1 Publication

    Catalytic activityi

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

    Cofactori

    Pyridoxal phosphate.By similarity

    Pathwayi

    GO - Molecular functioni

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

    GO - Biological processi

    1. photomorphogenesis Source: TAIR
    2. pollen development Source: TAIR
    3. sphingolipid biosynthetic process Source: TAIR

    Keywords - Molecular functioni

    Acyltransferase, Transferase

    Keywords - Biological processi

    Lipid metabolism, Sphingolipid metabolism

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciARA:AT3G48780-MONOMER.
    ReactomeiREACT_190876. Sphingolipid de novo biosynthesis.
    UniPathwayiUPA00222.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Long chain base biosynthesis protein 2b (EC:2.3.1.50)
    Short name:
    AtLCB2b
    Alternative name(s):
    Serine palmitoyltransferase 1
    Short name:
    AtSPT1
    Gene namesi
    Name:LCB2b
    Synonyms:LCB2.2, SPT1
    Ordered Locus Names:At3g48780
    ORF Names:T21J18_50
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G48780.

    Subcellular locationi

    GO - Cellular componenti

    1. endoplasmic reticulum membrane Source: UniProtKB-SubCell
    2. integral component of membrane Source: UniProtKB-KW

    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 2bPRO_0000419146Add
    BLAST

    Amino acid modifications

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

    Proteomic databases

    PRIDEiQ9M304.

    Expressioni

    Tissue specificityi

    Ubiquitous with the highest expression in flowers.1 Publication

    Developmental stagei

    In young flower buds was initially restricted to developing pollen spores within the stamen and is not detected in the petals, glumes or petiole until the flowers are mature.1 Publication

    Gene expression databases

    GenevestigatoriQ9M304.

    Interactioni

    Subunit structurei

    Heterodimer with LCB1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (LCB2a or LCB2b).1 Publication

    Protein-protein interaction databases

    STRINGi3702.AT3G48780.1-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9M304.
    SMRiQ9M304. Positions 69-469.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

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

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    HOGENOMiHOG000206826.
    InParanoidiQ9M304.
    KOiK00654.
    OMAiCADASEE.
    PhylomeDBiQ9M304.

    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.

    Q9M304-1 [UniParc]FASTAAdd to Basket

    « Hide

    MITIPYLTAV STYFSYGLLF AFGQLRDYSR LIFDWWRTNN LQGYAPICLA    50
    HEDFYIRRLY HRIQDCFGRP ISSAPDAWID VVERVSDDNN KTLKRTTKTS 100
    RCLNLGSYNY LGFGSFDEYC TPRVIESLKK FSASTCSSRV DAGTTSVHAE 150
    LEDCVAKYVG QPAAVIFGMG YATNSAIIPV LIGKGGLIIS DSLNHTSIVN 200
    GARGSGATIR VFQHNTPGHL EKVLKEQIAE GQPRTHRPWK KIIVVVEGIY 250
    SMEGEICHLP EIVSICKKYK AYVYLDEAHS IGAIGKTGRG VCELLGVDTS 300
    DVDIMMGTFT KSFGSCGGYI AGSKDLIQYL KHQCPAHLYA TSISTPSATQ 350
    IISAIKVILG EDGSNRGAQK LARIRENSNF FRAELQKMGF EVLGDNDSPV 400
    MPIMLYNPAK IPAFSRECLR ENLAVVVVGF PATPLLLARA RICISASHSR 450
    EDLIKALQVI SKAGDLTGIK YFPAAPKKQE VEKNGIKLD 489
    Length:489
    Mass (Da):53,863
    Last modified:October 1, 2000 - v1
    Checksum:iBE059A00F5632105
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB074928 mRNA. Translation: BAB78461.1.
    AL132963 Genomic DNA. Translation: CAB87906.1.
    CP002686 Genomic DNA. Translation: AEE78455.1.
    AY054489 mRNA. Translation: AAK96680.1.
    AY059882 mRNA. Translation: AAL24364.1.
    AY114662 mRNA. Translation: AAM47981.1.
    BT006615 mRNA. Translation: AAP31959.1.
    AK229667 mRNA. Translation: BAF01511.1.
    PIRiT49274.
    RefSeqiNP_190447.1. NM_114737.4.
    UniGeneiAt.1379.
    At.75040.

    Genome annotation databases

    EnsemblPlantsiAT3G48780.1; AT3G48780.1; AT3G48780.
    GeneIDi824039.
    KEGGiath:AT3G48780.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB074928 mRNA. Translation: BAB78461.1 .
    AL132963 Genomic DNA. Translation: CAB87906.1 .
    CP002686 Genomic DNA. Translation: AEE78455.1 .
    AY054489 mRNA. Translation: AAK96680.1 .
    AY059882 mRNA. Translation: AAL24364.1 .
    AY114662 mRNA. Translation: AAM47981.1 .
    BT006615 mRNA. Translation: AAP31959.1 .
    AK229667 mRNA. Translation: BAF01511.1 .
    PIRi T49274.
    RefSeqi NP_190447.1. NM_114737.4.
    UniGenei At.1379.
    At.75040.

    3D structure databases

    ProteinModelPortali Q9M304.
    SMRi Q9M304. Positions 69-469.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT3G48780.1-P.

    Proteomic databases

    PRIDEi Q9M304.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G48780.1 ; AT3G48780.1 ; AT3G48780 .
    GeneIDi 824039.
    KEGGi ath:AT3G48780.

    Organism-specific databases

    TAIRi AT3G48780.

    Phylogenomic databases

    HOGENOMi HOG000206826.
    InParanoidi Q9M304.
    KOi K00654.
    OMAi CADASEE.
    PhylomeDBi Q9M304.

    Enzyme and pathway databases

    UniPathwayi UPA00222 .
    BioCyci ARA:AT3G48780-MONOMER.
    Reactomei REACT_190876. Sphingolipid de novo biosynthesis.

    Miscellaneous databases

    PROi Q9M304.

    Gene expression databases

    Genevestigatori Q9M304.

    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. "A gene for serine palmitoyltransferase in Arabidopsis."
      Matsumura M., Mori J., Imai H.
      Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
      Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
      , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
      Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "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.
    5. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 244-489.
      Strain: cv. Columbia.
    6. "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.

    Entry informationi

    Entry nameiLCB2B_ARATH
    AccessioniPrimary (citable) accession number: Q9M304
    Secondary accession number(s): Q0WMY9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2012
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 99 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    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