LCB2A_ARATH
ID LCB2A_ARATH Reviewed; 489 AA.
AC Q9LSZ9; B9DFX8; Q9LRB4;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Long chain base biosynthesis protein 2a;
DE Short=AtLCB2a;
DE EC=2.3.1.50 {ECO:0000305|PubMed:11726713};
DE AltName: Full=Long chain base biosynthesis protein 2;
DE Short=AtLCB2;
GN Name=LCB2a; Synonyms=LCB2; OrderedLocusNames=At5g23670; ORFNames=MQM1.6;
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], AND TISSUE SPECIFICITY.
RX PubMed=11171191; DOI=10.1042/bst0280745;
RA Tamura K., Nishiura H., Mori J., Imai H.;
RT "Cloning and characterization of a cDNA encoding serine
RT palmitoyltransferase in Arabidopsis thaliana.";
RL Biochem. Soc. Trans. 28:745-747(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, TISSUE
RP SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=11726713; DOI=10.1093/pcp/pce165;
RA Tamura K., Mitsuhashi N., Hara-Nishimura I., Imai H.;
RT "Characterization of an Arabidopsis cDNA encoding a subunit of serine
RT palmitoyltransferase, the initial enzyme in sphingolipid biosynthesis.";
RL Plant Cell Physiol. 42:1274-1281(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
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] OF 248-489.
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 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, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND SUBUNIT.
RX PubMed=18208516; DOI=10.1111/j.1365-313x.2008.03420.x;
RA Dietrich C.R., Han G., Chen M., Berg R.H., Dunn T.M., Cahoon E.B.;
RT "Loss-of-function mutations and inducible RNAi suppression of Arabidopsis
RT LCB2 genes reveal the critical role of sphingolipids in gametophytic and
RT sporophytic cell viability.";
RL Plant J. 54:284-298(2008).
RN [9]
RP FUNCTION.
RX PubMed=21534970; DOI=10.1111/j.1469-8137.2011.03727.x;
RA Saucedo-Garcia M., Guevara-Garcia A., Gonzalez-Solis A., Cruz-Garcia F.,
RA Vazquez-Santana S., Markham J.E., Lozano-Rosas M.G., Dietrich C.R.,
RA Ramos-Vega M., Cahoon E.B., Gavilanes-Ruiz M.;
RT "MPK6, sphinganine and the LCB2a gene from serine palmitoyltransferase are
RT required in the signaling pathway that mediates cell death induced by long
RT chain bases in Arabidopsis.";
RL New Phytol. 191:943-957(2011).
CC -!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed
CC with LCB1 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:11726713, ECO:0000269|PubMed:18208516,
CC ECO:0000269|PubMed:21534970}.
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 Evidence={ECO:0000305|PubMed:11726713};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
CC {ECO:0000305|PubMed:11726713}.
CC -!- SUBUNIT: Heterodimer with LCB1. Component of the serine
CC palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (LCB2a or
CC LCB2b). {ECO:0000269|PubMed:17194770, ECO:0000269|PubMed:18208516}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:11726713}; Single-pass membrane protein
CC {ECO:0000269|PubMed:11726713}.
CC -!- TISSUE SPECIFICITY: Ubiquitous. Detected in leaves, roots, stems,
CC flowers and at a lower level in mature seeds.
CC {ECO:0000269|PubMed:11171191, ECO:0000269|PubMed:11726713,
CC ECO:0000269|PubMed:18208516}.
CC -!- DEVELOPMENTAL STAGE: Detected at high levels in the petiole, sepals and
CC petals in young flowers, but was not detected in the anthers during the
CC early stages of pollen development. {ECO:0000269|PubMed:18208516}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype. Lcb2a and lcb2b double
CC mutant is not viable due to pollen lethality.
CC {ECO:0000269|PubMed:18208516}.
CC -!- MISCELLANEOUS: The lcb2a-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 ---------------------------------------------------------------------------
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; AB046384; BAB03231.1; -; mRNA.
DR EMBL; AB025633; BAA97234.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93196.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93197.1; -; Genomic_DNA.
DR EMBL; AY050829; AAK92764.1; -; mRNA.
DR EMBL; AY133827; AAM91761.1; -; mRNA.
DR EMBL; AK316942; BAH19645.1; -; mRNA.
DR RefSeq; NP_001031932.1; NM_001036855.1.
DR RefSeq; NP_197756.1; NM_122272.3.
DR AlphaFoldDB; Q9LSZ9; -.
DR SMR; Q9LSZ9; -.
DR BioGRID; 17707; 1.
DR STRING; 3702.AT5G23670.1; -.
DR PaxDb; Q9LSZ9; -.
DR PRIDE; Q9LSZ9; -.
DR ProteomicsDB; 237130; -.
DR EnsemblPlants; AT5G23670.1; AT5G23670.1; AT5G23670.
DR EnsemblPlants; AT5G23670.2; AT5G23670.2; AT5G23670.
DR GeneID; 832432; -.
DR Gramene; AT5G23670.1; AT5G23670.1; AT5G23670.
DR Gramene; AT5G23670.2; AT5G23670.2; AT5G23670.
DR KEGG; ath:AT5G23670; -.
DR Araport; AT5G23670; -.
DR TAIR; locus:2171731; AT5G23670.
DR eggNOG; KOG1357; Eukaryota.
DR HOGENOM; CLU_015846_7_0_1; -.
DR InParanoid; Q9LSZ9; -.
DR OMA; IEDEPPY; -.
DR OrthoDB; 438936at2759; -.
DR PhylomeDB; Q9LSZ9; -.
DR BioCyc; ARA:AT5G23670-MON; -.
DR BioCyc; MetaCyc:AT5G23670-MON; -.
DR BRENDA; 2.3.1.50; 399.
DR UniPathway; UPA00222; -.
DR PRO; PR:Q9LSZ9; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LSZ9; baseline and differential.
DR Genevisible; Q9LSZ9; AT.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0016020; C:membrane; IDA:TAIR.
DR GO; GO:0017059; C:serine C-palmitoyltransferase complex; IBA:GO_Central.
DR GO; GO:0005773; C:vacuole; HDA:TAIR.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0004758; F:serine C-palmitoyltransferase activity; IDA:TAIR.
DR GO; GO:0046513; P:ceramide biosynthetic process; IBA:GO_Central.
DR GO; GO:0009640; P:photomorphogenesis; IMP:TAIR.
DR GO; GO:0009555; P:pollen development; IMP:TAIR.
DR GO; GO:0043067; P:regulation of programmed cell death; IMP:UniProtKB.
DR GO; GO:0046512; P:sphingosine biosynthetic process; IDA:TAIR.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR001917; Aminotrans_II_pyridoxalP_BS.
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.
DR PROSITE; PS00599; AA_TRANSFER_CLASS_2; 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..489
FT /note="Long chain base biosynthesis protein 2a"
FT /id="PRO_0000419145"
FT TRANSMEM 2..22
FT /note="Helical"
FT /evidence="ECO:0000255"
FT MOD_RES 311
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT CONFLICT 65
FT /note="D -> N (in Ref. 1 and 2; BAB03231)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 489 AA; 54290 MW; 00B396BB47D2E048 CRC64;
MITIPYLTAV STYFSYGLLF AFGQLRDFFR RFIDWWFTSN LQGYAPICLG HEDFYIRRLY
HRIQDCFERP ISSAPDAWFD VVERYSNDNN KTLKRTTKTS RCLNLGSYNY LGFGSFDEYC
TPRVIESLKK FSASTCSSRV DAGTTSVHAE LEECVTRFVG KPAAVVFGMG YATNSAIIPV
LIGKGGLIIS DSLNHSSIVN GARGSGATIR VFQHNTPSHL ERVLREQIAE GQPRTHRPWK
KIIVVVEGIY SMEGEICHLP EVVAICKKYK AYVYLDEAHS IGAIGKTGKG ICELLGVDTA
DVDVMMGTFT KSFGSCGGYI AGSKELIQYL KHQCPAHLYA TSIPTPSAQQ IISAIKVILG
EDGSNRGAQK LARIRENSNF FRAELQKMGF EVLGDNDSPV MPIMLYNPAK IPAFSRECLR
QKVAVVVVGF PATPLLLARA RICISASHSR EDLIRALKVI SKVGDLSGIK YFPAEPKKIE
QSKNDIKLD
