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Q94IB8

- LCB1_ARATH

UniProt

Q94IB8 - LCB1_ARATH

Protein

Long chain base biosynthesis protein 1

Gene

LCB1

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 91 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    Functioni

    Serine palmitoyltransferase (SPT). The heterodimer formed with LCB2 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. cell growth Source: TAIR
    3. regulation of programmed cell death Source: UniProtKB
    4. sphingolipid 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:AT4G36480-MONOMER.
    ARA:GQT-1717-MONOMER.
    MetaCyc:AT4G36480-MONOMER.
    ReactomeiREACT_190876. Sphingolipid de novo biosynthesis.
    UniPathwayiUPA00222.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Long chain base biosynthesis protein 1 (EC:2.3.1.50)
    Short name:
    AtLCB1
    Alternative name(s):
    Protein EMBRYO DEFECTIVE 2779
    Protein FUMONISIN B1 RESISTANT 11
    Gene namesi
    Name:LCB1
    Synonyms:EMB2779, FBR11
    Ordered Locus Names:At4g36480
    ORF Names:AP22, C7A10.880
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 4

    Organism-specific databases

    TAIRiAT4G36480.

    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

    Keywords - Cellular componenti

    Endoplasmic reticulum, Membrane

    Pathology & Biotechi

    Disruption phenotypei

    Defective Embryo and pollen lethality. RNAi mutants display plant size reduction, altered leaf morphology and increases in relative amounts of saturated sphingolipid long-chain bases.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 482482Long chain base biosynthesis protein 1PRO_0000419144Add
    BLAST

    Proteomic databases

    PRIDEiQ94IB8.

    Expressioni

    Tissue specificityi

    Ubiquitous.1 Publication

    Gene expression databases

    GenevestigatoriQ94IB8.

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    IntActiQ94IB8. 2 interactions.
    STRINGi3702.AT4G36480.2-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ94IB8.
    SMRiQ94IB8. Positions 95-478.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei32 – 5221HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG0156.
    HOGENOMiHOG000216602.
    InParanoidiQ94IB8.
    KOiK00654.
    OMAiTGPPSHK.
    PhylomeDBiQ94IB8.

    Family and domain databases

    Gene3Di3.40.640.10. 1 hit.
    InterProiIPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view]
    PfamiPF00155. Aminotran_1_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q94IB8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASNLVEMFN AALNWVTMIL ESPSARVVLF GVPIRGHFFV EGLLGVVIII    50
    LLTRKSYKPP KRPLTEQEID ELCDEWVPEP LIPPITEDMK HEPPVLESAA 100
    GPHTTVNGKD VVNFASANYL GLIGHEKLLE SCTSALEKYG VGSCGPRGFY 150
    GTIDVHLDCE TRISKFLGTP DSILYSYGLS TMFSTIPCFC KKGDVIVADE 200
    GVHWGIQNGL QLSRSTIVYF KHNDMESLRI TLEKIMTKYK RSKNLRRYIV 250
    AEAVYQNSGQ IAPLDEIVKL KEKYRFRVIL DESNSFGVLG RSGRGLAEHH 300
    SVPIEKIDVV TAAMGHALAT EGGFCTGNAR IIDYQRLSSS GYVFSASLPP 350
    YLASAAITAI DVIDQNPDML VKLKQNVALL WKGLSDIKGM SLTSNRESPI 400
    VFLKLEKSSG SAKDDLLLLE KMADRALKED SLLVVSSKRS FLDKCRLPVG 450
    IKLYVSAGHS ESDLLKASES LKRLASELLL KS 482
    Length:482
    Mass (Da):53,141
    Last modified:December 1, 2001 - v1
    Checksum:iCE23247C3F7ADE28
    GO

    Sequence cautioni

    The sequence CAB16844.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence CAB80314.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti306 – 3061K → E in BAH20117. (PubMed:19423640)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB063254 mRNA. Translation: BAB60898.1.
    Z99708 Genomic DNA. Translation: CAB16844.1. Sequence problems.
    AL161589 Genomic DNA. Translation: CAB80314.1. Sequence problems.
    CP002687 Genomic DNA. Translation: AEE86660.1.
    CP002687 Genomic DNA. Translation: AEE86661.1.
    AY120759 mRNA. Translation: AAM53317.1.
    BT000131 mRNA. Translation: AAN15450.1.
    AK317450 mRNA. Translation: BAH20117.1.
    PIRiF85430.
    RefSeqiNP_001031796.1. NM_001036719.1.
    NP_568005.1. NM_119811.2.
    UniGeneiAt.22137.

    Genome annotation databases

    EnsemblPlantsiAT4G36480.1; AT4G36480.1; AT4G36480.
    AT4G36480.2; AT4G36480.2; AT4G36480.
    GeneIDi829800.
    KEGGiath:AT4G36480.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB063254 mRNA. Translation: BAB60898.1 .
    Z99708 Genomic DNA. Translation: CAB16844.1 . Sequence problems.
    AL161589 Genomic DNA. Translation: CAB80314.1 . Sequence problems.
    CP002687 Genomic DNA. Translation: AEE86660.1 .
    CP002687 Genomic DNA. Translation: AEE86661.1 .
    AY120759 mRNA. Translation: AAM53317.1 .
    BT000131 mRNA. Translation: AAN15450.1 .
    AK317450 mRNA. Translation: BAH20117.1 .
    PIRi F85430.
    RefSeqi NP_001031796.1. NM_001036719.1.
    NP_568005.1. NM_119811.2.
    UniGenei At.22137.

    3D structure databases

    ProteinModelPortali Q94IB8.
    SMRi Q94IB8. Positions 95-478.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q94IB8. 2 interactions.
    STRINGi 3702.AT4G36480.2-P.

    Proteomic databases

    PRIDEi Q94IB8.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G36480.1 ; AT4G36480.1 ; AT4G36480 .
    AT4G36480.2 ; AT4G36480.2 ; AT4G36480 .
    GeneIDi 829800.
    KEGGi ath:AT4G36480.

    Organism-specific databases

    TAIRi AT4G36480.

    Phylogenomic databases

    eggNOGi COG0156.
    HOGENOMi HOG000216602.
    InParanoidi Q94IB8.
    KOi K00654.
    OMAi TGPPSHK.
    PhylomeDBi Q94IB8.

    Enzyme and pathway databases

    UniPathwayi UPA00222 .
    BioCyci ARA:AT4G36480-MONOMER.
    ARA:GQT-1717-MONOMER.
    MetaCyc:AT4G36480-MONOMER.
    Reactomei REACT_190876. Sphingolipid de novo biosynthesis.

    Miscellaneous databases

    PROi Q94IB8.

    Gene expression databases

    Genevestigatori Q94IB8.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    InterProi IPR004839. Aminotransferase_I/II.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view ]
    Pfami PF00155. Aminotran_1_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53383. SSF53383. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of a cDNA encoding a subunit of serine palmitoyltransferase."
      Mori J., Tamura K., Nishiura H., Morimoto Y., Imai H.
      Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana."
      Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C., Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P., Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.
      , Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R., De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M., Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M., Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A., Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D., Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A., Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S., Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G., Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.
      Nature 391:485-488(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
      Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
      , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
      Nature 402:769-777(1999) [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].
      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: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, SUBUNIT.
    8. "Involvement of sphingoid bases in mediating reactive oxygen intermediate production and programmed cell death in Arabidopsis."
      Shi L., Bielawski J., Mu J., Dong H., Teng C., Zhang J., Yang X., Tomishige N., Hanada K., Hannun Y.A., Zuo J.
      Cell Res. 17:1030-1040(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis."
      Teng C., Dong H., Shi L., Deng Y., Mu J., Zhang J., Yang X., Zuo J.
      Plant Physiol. 146:1322-1332(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.

    Entry informationi

    Entry nameiLCB1_ARATH
    AccessioniPrimary (citable) accession number: Q94IB8
    Secondary accession number(s): B9DHA0, O23233
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2012
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 91 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The fbr11-1 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