LCB2B_ARATH
ID LCB2B_ARATH Reviewed; 489 AA.
AC Q9M304; Q0WMY9;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Long chain base biosynthesis protein 2b;
DE Short=AtLCB2b;
DE EC=2.3.1.50 {ECO:0000305|PubMed:18208516};
DE AltName: Full=Serine palmitoyltransferase 1;
DE Short=AtSPT1;
GN Name=LCB2b; Synonyms=LCB2.2, SPT1; OrderedLocusNames=At3g48780;
GN ORFNames=T21J18_50;
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 Matsumura M., Mori J., Imai H.;
RT "A gene for serine palmitoyltransferase in Arabidopsis.";
RL Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 244-489.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, 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).
CC -!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed
CC with LCB1 constitutes the catalytic core. Plays an important role
CC during male gametogenesis and embryogenesis.
CC {ECO:0000269|PubMed:18208516}.
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:18208516};
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:18208516}.
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:18208516}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane {ECO:0000250};
CC Single-pass membrane protein {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Ubiquitous with the highest expression in flowers.
CC {ECO:0000269|PubMed:18208516}.
CC -!- DEVELOPMENTAL STAGE: In young flower buds was initially restricted to
CC developing pollen spores within the stamen and is not detected in the
CC petals, glumes or petiole until the flowers are mature.
CC {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 -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; AB074928; BAB78461.1; -; mRNA.
DR EMBL; AL132963; CAB87906.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78455.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM63778.1; -; Genomic_DNA.
DR EMBL; AY054489; AAK96680.1; -; mRNA.
DR EMBL; AY059882; AAL24364.1; -; mRNA.
DR EMBL; AY114662; AAM47981.1; -; mRNA.
DR EMBL; BT006615; AAP31959.1; -; mRNA.
DR EMBL; AK229667; BAF01511.1; -; mRNA.
DR PIR; T49274; T49274.
DR RefSeq; NP_001325849.1; NM_001339379.1.
DR RefSeq; NP_190447.1; NM_114737.5.
DR AlphaFoldDB; Q9M304; -.
DR SMR; Q9M304; -.
DR STRING; 3702.AT3G48780.1; -.
DR PaxDb; Q9M304; -.
DR PRIDE; Q9M304; -.
DR ProteomicsDB; 237131; -.
DR EnsemblPlants; AT3G48780.1; AT3G48780.1; AT3G48780.
DR EnsemblPlants; AT3G48780.2; AT3G48780.2; AT3G48780.
DR GeneID; 824039; -.
DR Gramene; AT3G48780.1; AT3G48780.1; AT3G48780.
DR Gramene; AT3G48780.2; AT3G48780.2; AT3G48780.
DR KEGG; ath:AT3G48780; -.
DR Araport; AT3G48780; -.
DR TAIR; locus:2099428; AT3G48780.
DR eggNOG; KOG1357; Eukaryota.
DR HOGENOM; CLU_015846_7_0_1; -.
DR InParanoid; Q9M304; -.
DR OMA; YPYFRPI; -.
DR OrthoDB; 438936at2759; -.
DR PhylomeDB; Q9M304; -.
DR BioCyc; ARA:AT3G48780-MON; -.
DR UniPathway; UPA00222; -.
DR PRO; PR:Q9M304; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M304; baseline and differential.
DR Genevisible; Q9M304; AT.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0017059; C:serine C-palmitoyltransferase complex; IBA:GO_Central.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0004758; F:serine C-palmitoyltransferase activity; IGI:UniProtKB.
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:0030148; P:sphingolipid biosynthetic process; IMP: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; 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; Endoplasmic reticulum; Lipid metabolism; Membrane;
KW Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
KW Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..489
FT /note="Long chain base biosynthesis protein 2b"
FT /id="PRO_0000419146"
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"
SQ SEQUENCE 489 AA; 53863 MW; BE059A00F5632105 CRC64;
MITIPYLTAV STYFSYGLLF AFGQLRDYSR LIFDWWRTNN LQGYAPICLA HEDFYIRRLY
HRIQDCFGRP ISSAPDAWID VVERVSDDNN KTLKRTTKTS RCLNLGSYNY LGFGSFDEYC
TPRVIESLKK FSASTCSSRV DAGTTSVHAE LEDCVAKYVG QPAAVIFGMG YATNSAIIPV
LIGKGGLIIS DSLNHTSIVN GARGSGATIR VFQHNTPGHL EKVLKEQIAE GQPRTHRPWK
KIIVVVEGIY SMEGEICHLP EIVSICKKYK AYVYLDEAHS IGAIGKTGRG VCELLGVDTS
DVDIMMGTFT KSFGSCGGYI AGSKDLIQYL KHQCPAHLYA TSISTPSATQ IISAIKVILG
EDGSNRGAQK LARIRENSNF FRAELQKMGF EVLGDNDSPV MPIMLYNPAK IPAFSRECLR
ENLAVVVVGF PATPLLLARA RICISASHSR EDLIKALQVI SKAGDLTGIK YFPAAPKKQE
VEKNGIKLD
