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Long chain base biosynthesis protein 2b (AtLCB2b) (EC 2.3.1.50) (Serine palmitoyltransferase 1) (AtSPT1)

 LCB2B_ARATH             Reviewed;         489 AA.
Q9M304; Q0WMY9;
03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
25-APR-2018, entry version 123.
RecName: Full=Long chain base biosynthesis protein 2b;
Short=AtLCB2b;
EC=2.3.1.50;
AltName: Full=Serine palmitoyltransferase 1;
Short=AtSPT1;
Name=LCB2b; Synonyms=LCB2.2, SPT1; OrderedLocusNames=At3g48780;
ORFNames=T21J18_50;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
Matsumura M., Mori J., Imai H.;
"A gene for serine palmitoyltransferase in Arabidopsis.";
Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130713; DOI=10.1038/35048706;
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.;
"Sequence and analysis of chromosome 3 of the plant Arabidopsis
thaliana.";
Nature 408:820-822(2000).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
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.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 244-489.
STRAIN=cv. Columbia;
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.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
[6]
FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL
STAGE, AND SUBUNIT.
PubMed=18208516; DOI=10.1111/j.1365-313X.2008.03420.x;
Dietrich C.R., Han G., Chen M., Berg R.H., Dunn T.M., Cahoon E.B.;
"Loss-of-function mutations and inducible RNAi suppression of
Arabidopsis LCB2 genes reveal the critical role of sphingolipids in
gametophytic and sporophytic cell viability.";
Plant J. 54:284-298(2008).
-!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer
formed with LCB1 constitutes the catalytic core. Plays an
important role during male gametogenesis and embryogenesis.
{ECO:0000269|PubMed:18208516}.
-!- CATALYTIC ACTIVITY: Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-
sphinganine + CO(2).
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000250};
-!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
-!- SUBUNIT: Heterodimer with LCB1. Component of the serine
palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2
(LCB2a or LCB2b). {ECO:0000269|PubMed:18208516}.
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
{ECO:0000250}; Single-pass membrane protein {ECO:0000250}.
-!- TISSUE SPECIFICITY: Ubiquitous with the highest expression in
flowers. {ECO:0000269|PubMed:18208516}.
-!- DEVELOPMENTAL STAGE: 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.
{ECO:0000269|PubMed:18208516}.
-!- DISRUPTION PHENOTYPE: No visible phenotype. Lcb2a and lcb2b double
mutant is not viable due to pollen lethality.
{ECO:0000269|PubMed:18208516}.
-!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
aminotransferase family. {ECO:0000305}.
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EMBL; AB074928; BAB78461.1; -; mRNA.
EMBL; AL132963; CAB87906.1; -; Genomic_DNA.
EMBL; CP002686; AEE78455.1; -; Genomic_DNA.
EMBL; CP002686; ANM63778.1; -; Genomic_DNA.
EMBL; AY054489; AAK96680.1; -; mRNA.
EMBL; AY059882; AAL24364.1; -; mRNA.
EMBL; AY114662; AAM47981.1; -; mRNA.
EMBL; BT006615; AAP31959.1; -; mRNA.
EMBL; AK229667; BAF01511.1; -; mRNA.
PIR; T49274; T49274.
RefSeq; NP_001325849.1; NM_001339379.1.
RefSeq; NP_190447.1; NM_114737.5.
UniGene; At.1379; -.
UniGene; At.75040; -.
ProteinModelPortal; Q9M304; -.
SMR; Q9M304; -.
STRING; 3702.AT3G48780.1; -.
PaxDb; Q9M304; -.
EnsemblPlants; AT3G48780.1; AT3G48780.1; AT3G48780.
EnsemblPlants; AT3G48780.2; AT3G48780.2; AT3G48780.
GeneID; 824039; -.
Gramene; AT3G48780.1; AT3G48780.1; AT3G48780.
Gramene; AT3G48780.2; AT3G48780.2; AT3G48780.
KEGG; ath:AT3G48780; -.
Araport; AT3G48780; -.
TAIR; locus:2099428; AT3G48780.
eggNOG; KOG1357; Eukaryota.
eggNOG; COG0156; LUCA.
HOGENOM; HOG000206826; -.
InParanoid; Q9M304; -.
KO; K00654; -.
OMA; TLNMSSY; -.
OrthoDB; EOG0936074X; -.
PhylomeDB; Q9M304; -.
BioCyc; ARA:AT3G48780-MONOMER; -.
UniPathway; UPA00222; -.
PRO; PR:Q9M304; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q9M304; baseline and differential.
Genevisible; Q9M304; AT.
GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
GO; GO:0004758; F:serine C-palmitoyltransferase activity; IGI:UniProtKB.
GO; GO:0009640; P:photomorphogenesis; IMP:TAIR.
GO; GO:0009555; P:pollen development; IMP:TAIR.
GO; GO:0030148; P:sphingolipid biosynthetic process; IMP:TAIR.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 2.
InterPro; IPR001917; Aminotrans_II_pyridoxalP_BS.
InterPro; IPR004839; Aminotransferase_I/II.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
Pfam; PF00155; Aminotran_1_2; 1.
SUPFAM; SSF53383; SSF53383; 1.
PROSITE; PS00599; AA_TRANSFER_CLASS_2; 1.
1: Evidence at protein level;
Acyltransferase; Complete proteome; Endoplasmic reticulum;
Lipid metabolism; Membrane; Pyridoxal phosphate; Reference proteome;
Sphingolipid metabolism; Transferase; Transmembrane;
Transmembrane helix.
CHAIN 1 489 Long chain base biosynthesis protein 2b.
/FTId=PRO_0000419146.
TRANSMEM 2 22 Helical. {ECO:0000255}.
MOD_RES 311 311 N6-(pyridoxal phosphate)lysine.
{ECO:0000250}.
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


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