LCB1_ARATH
ID LCB1_ARATH Reviewed; 482 AA.
AC Q94IB8; B9DHA0; O23233;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Long chain base biosynthesis protein 1;
DE Short=AtLCB1;
DE EC=2.3.1.50;
DE AltName: Full=Protein EMBRYO DEFECTIVE 2779;
DE AltName: Full=Protein FUMONISIN B1 RESISTANT 11;
GN Name=LCB1; Synonyms=EMB2779, FBR11; OrderedLocusNames=At4g36480;
GN ORFNames=AP22, C7A10.880;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Mori J., Tamura K., Nishiura H., Morimoto Y., Imai H.;
RT "Cloning and characterization of a cDNA encoding a subunit of serine
RT palmitoyltransferase.";
RL Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, SUBCELLULAR LOCATION,
RP AND SUBUNIT.
RX PubMed=17194770; DOI=10.1105/tpc.105.040774;
RA Chen M., Han G., Dietrich C.R., Dunn T.M., Cahoon E.B.;
RT "The essential nature of sphingolipids in plants as revealed by the
RT functional identification and characterization of the Arabidopsis LCB1
RT subunit of serine palmitoyltransferase.";
RL Plant Cell 18:3576-3593(2006).
RN [8]
RP FUNCTION.
RX PubMed=18059378; DOI=10.1038/cr.2007.100;
RA Shi L., Bielawski J., Mu J., Dong H., Teng C., Zhang J., Yang X.,
RA Tomishige N., Hanada K., Hannun Y.A., Zuo J.;
RT "Involvement of sphingoid bases in mediating reactive oxygen intermediate
RT production and programmed cell death in Arabidopsis.";
RL Cell Res. 17:1030-1040(2007).
RN [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=18218968; DOI=10.1104/pp.107.113506;
RA Teng C., Dong H., Shi L., Deng Y., Mu J., Zhang J., Yang X., Zuo J.;
RT "Serine palmitoyltransferase, a key enzyme for de novo synthesis of
RT sphingolipids, is essential for male gametophyte development in
RT Arabidopsis.";
RL Plant Physiol. 146:1322-1332(2008).
CC -!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed
CC with LCB2 constitutes the catalytic core. Involved in the regulation of
CC the programmed cell death (PCD) signaling pathway. Plays an important
CC role during male gametogenesis and embryogenesis.
CC {ECO:0000269|PubMed:17194770, ECO:0000269|PubMed:18059378,
CC ECO:0000269|PubMed:18218968}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + hexadecanoyl-CoA + L-serine = 3-oxosphinganine + CO2 +
CC CoA; Xref=Rhea:RHEA:14761, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:33384, ChEBI:CHEBI:57287, ChEBI:CHEBI:57379,
CC ChEBI:CHEBI:58299; EC=2.3.1.50;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
CC -!- SUBUNIT: Heterodimer with LCB2 (LCB2a or LCB2b). Component of the
CC serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2
CC (LCB2a or LCB2b). {ECO:0000269|PubMed:17194770}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:17194770}; Single-pass membrane protein
CC {ECO:0000269|PubMed:17194770}.
CC -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:17194770}.
CC -!- DISRUPTION PHENOTYPE: Defective Embryo and pollen lethality. RNAi
CC mutants display plant size reduction, altered leaf morphology and
CC increases in relative amounts of saturated sphingolipid long-chain
CC bases. {ECO:0000269|PubMed:17194770, ECO:0000269|PubMed:18218968}.
CC -!- MISCELLANEOUS: The fbr11-1 mutant is incapable of initiating programmed
CC cell death (PCD) after induction by fumonisin B1 (FB1), a specific
CC inhibitor of ceramide synthase.
CC -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB16844.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80314.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB063254; BAB60898.1; -; mRNA.
DR EMBL; Z99708; CAB16844.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161589; CAB80314.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86660.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86661.1; -; Genomic_DNA.
DR EMBL; AY120759; AAM53317.1; -; mRNA.
DR EMBL; BT000131; AAN15450.1; -; mRNA.
DR EMBL; AK317450; BAH20117.1; -; mRNA.
DR PIR; F85430; F85430.
DR RefSeq; NP_001031796.1; NM_001036719.2.
DR RefSeq; NP_568005.1; NM_119811.3.
DR AlphaFoldDB; Q94IB8; -.
DR SMR; Q94IB8; -.
DR BioGRID; 15082; 7.
DR IntAct; Q94IB8; 2.
DR STRING; 3702.AT4G36480.1; -.
DR PaxDb; Q94IB8; -.
DR PRIDE; Q94IB8; -.
DR ProteomicsDB; 250753; -.
DR EnsemblPlants; AT4G36480.1; AT4G36480.1; AT4G36480.
DR EnsemblPlants; AT4G36480.2; AT4G36480.2; AT4G36480.
DR GeneID; 829800; -.
DR Gramene; AT4G36480.1; AT4G36480.1; AT4G36480.
DR Gramene; AT4G36480.2; AT4G36480.2; AT4G36480.
DR KEGG; ath:AT4G36480; -.
DR Araport; AT4G36480; -.
DR TAIR; locus:2115350; AT4G36480.
DR eggNOG; KOG1358; Eukaryota.
DR HOGENOM; CLU_015846_0_1_1; -.
DR InParanoid; Q94IB8; -.
DR OMA; RNTPTFA; -.
DR OrthoDB; 438936at2759; -.
DR PhylomeDB; Q94IB8; -.
DR BioCyc; ARA:AT4G36480-MON; -.
DR BioCyc; MetaCyc:AT4G36480-MON; -.
DR BRENDA; 2.3.1.50; 399.
DR UniPathway; UPA00222; -.
DR PRO; PR:Q94IB8; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94IB8; baseline and differential.
DR Genevisible; Q94IB8; AT.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0004758; F:serine C-palmitoyltransferase activity; IBA:GO_Central.
DR GO; GO:0046513; P:ceramide biosynthetic process; IBA:GO_Central.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0009825; P:multidimensional cell growth; IMP:TAIR.
DR GO; GO:0043067; P:regulation of programmed cell death; IMP:UniProtKB.
DR GO; GO:0030148; P:sphingolipid biosynthetic process; TAS:TAIR.
DR GO; GO:0046512; P:sphingosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR004839; Aminotransferase_I/II.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW Acyltransferase; Apoptosis; Endoplasmic reticulum; Lipid metabolism;
KW Membrane; Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
KW Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..482
FT /note="Long chain base biosynthesis protein 1"
FT /id="PRO_0000419144"
FT TRANSMEM 32..52
FT /note="Helical"
FT /evidence="ECO:0000255"
FT CONFLICT 306
FT /note="K -> E (in Ref. 6; BAH20117)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 482 AA; 53141 MW; CE23247C3F7ADE28 CRC64;
MASNLVEMFN AALNWVTMIL ESPSARVVLF GVPIRGHFFV EGLLGVVIII LLTRKSYKPP
KRPLTEQEID ELCDEWVPEP LIPPITEDMK HEPPVLESAA GPHTTVNGKD VVNFASANYL
GLIGHEKLLE SCTSALEKYG VGSCGPRGFY GTIDVHLDCE TRISKFLGTP DSILYSYGLS
TMFSTIPCFC KKGDVIVADE GVHWGIQNGL QLSRSTIVYF KHNDMESLRI TLEKIMTKYK
RSKNLRRYIV AEAVYQNSGQ IAPLDEIVKL KEKYRFRVIL DESNSFGVLG RSGRGLAEHH
SVPIEKIDVV TAAMGHALAT EGGFCTGNAR IIDYQRLSSS GYVFSASLPP YLASAAITAI
DVIDQNPDML VKLKQNVALL WKGLSDIKGM SLTSNRESPI VFLKLEKSSG SAKDDLLLLE
KMADRALKED SLLVVSSKRS FLDKCRLPVG IKLYVSAGHS ESDLLKASES LKRLASELLL
KS
