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Long chain base biosynthesis protein 2a (AtLCB2a) (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (AtLCB2)

 LCB2A_ARATH             Reviewed;         489 AA.
Q9LSZ9; B9DFX8; Q9LRB4;
03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
05-DEC-2018, entry version 129.
RecName: Full=Long chain base biosynthesis protein 2a;
Short=AtLCB2a;
EC=2.3.1.50;
AltName: Full=Long chain base biosynthesis protein 2;
Short=AtLCB2;
Name=LCB2a; Synonyms=LCB2; OrderedLocusNames=At5g23670;
ORFNames=MQM1.6;
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], AND TISSUE SPECIFICITY.
PubMed=11171191; DOI=10.1042/bst0280745;
Tamura K., Nishiura H., Mori J., Imai H.;
"Cloning and characterization of a cDNA encoding serine
palmitoyltransferase in Arabidopsis thaliana.";
Biochem. Soc. Trans. 28:745-747(2000).
[2]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND
SUBCELLULAR LOCATION.
PubMed=11726713; DOI=10.1093/pcp/pce165;
Tamura K., Mitsuhashi N., Hara-Nishimura I., Imai H.;
"Characterization of an Arabidopsis cDNA encoding a subunit of serine
palmitoyltransferase, the initial enzyme in sphingolipid
biosynthesis.";
Plant Cell Physiol. 42:1274-1281(2001).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10718197; DOI=10.1093/dnares/7.1.31;
Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
features of the regions of 3,076,755 bp covered by sixty P1 and TAC
clones.";
DNA Res. 7:31-63(2000).
[4]
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).
[5]
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).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 248-489.
STRAIN=cv. Columbia; TISSUE=Rosette leaf;
PubMed=19423640; DOI=10.1093/dnares/dsp009;
Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M.,
Seki M., Shinozaki K.;
"Analysis of multiple occurrences of alternative splicing events in
Arabidopsis thaliana using novel sequenced full-length cDNAs.";
DNA Res. 16:155-164(2009).
[7]
SUBUNIT.
PubMed=17194770; DOI=10.1105/tpc.105.040774;
Chen M., Han G., Dietrich C.R., Dunn T.M., Cahoon E.B.;
"The essential nature of sphingolipids in plants as revealed by the
functional identification and characterization of the Arabidopsis LCB1
subunit of serine palmitoyltransferase.";
Plant Cell 18:3576-3593(2006).
[8]
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).
[9]
FUNCTION.
PubMed=21534970; DOI=10.1111/j.1469-8137.2011.03727.x;
Saucedo-Garcia M., Guevara-Garcia A., Gonzalez-Solis A.,
Cruz-Garcia F., Vazquez-Santana S., Markham J.E., Lozano-Rosas M.G.,
Dietrich C.R., Ramos-Vega M., Cahoon E.B., Gavilanes-Ruiz M.;
"MPK6, sphinganine and the LCB2a gene from serine palmitoyltransferase
are required in the signaling pathway that mediates cell death induced
by long chain bases in Arabidopsis.";
New Phytol. 191:943-957(2011).
-!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer
formed with LCB1 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. {ECO:0000269|PubMed:11726713,
ECO:0000269|PubMed:18208516, ECO:0000269|PubMed:21534970}.
-!- CATALYTIC ACTIVITY:
Reaction=H(+) + hexadecanoyl-CoA + L-serine = 3-oxosphinganine +
CO2 + CoA; Xref=Rhea:RHEA:14761, ChEBI:CHEBI:15378,
ChEBI:CHEBI:16526, ChEBI:CHEBI:33384, ChEBI:CHEBI:57287,
ChEBI:CHEBI:57379, ChEBI:CHEBI:58299; EC=2.3.1.50;
-!- 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:17194770,
ECO:0000269|PubMed:18208516}.
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
{ECO:0000269|PubMed:11726713}; Single-pass membrane protein
{ECO:0000269|PubMed:11726713}.
-!- TISSUE SPECIFICITY: Ubiquitous. Detected in leaves, roots, stems,
flowers and at a lower level in mature seeds.
{ECO:0000269|PubMed:11171191, ECO:0000269|PubMed:11726713,
ECO:0000269|PubMed:18208516}.
-!- DEVELOPMENTAL STAGE: Detected at high levels in the petiole,
sepals and petals in young flowers, but was not detected in the
anthers during the early stages of pollen development.
{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}.
-!- MISCELLANEOUS: The lcb2a-1 mutant is incapable of initiating
programmed cell death (PCD) after induction by fumonisin B1 (FB1),
a specific inhibitor of ceramide synthase.
-!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
aminotransferase family. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AB046384; BAB03231.1; -; mRNA.
EMBL; AB025633; BAA97234.1; -; Genomic_DNA.
EMBL; CP002688; AED93196.1; -; Genomic_DNA.
EMBL; CP002688; AED93197.1; -; Genomic_DNA.
EMBL; AY050829; AAK92764.1; -; mRNA.
EMBL; AY133827; AAM91761.1; -; mRNA.
EMBL; AK316942; BAH19645.1; -; mRNA.
RefSeq; NP_001031932.1; NM_001036855.1.
RefSeq; NP_197756.1; NM_122272.3.
UniGene; At.23395; -.
UniGene; At.49054; -.
ProteinModelPortal; Q9LSZ9; -.
SMR; Q9LSZ9; -.
BioGrid; 17707; 1.
STRING; 3702.AT5G23670.1; -.
PaxDb; Q9LSZ9; -.
EnsemblPlants; AT5G23670.1; AT5G23670.1; AT5G23670.
EnsemblPlants; AT5G23670.2; AT5G23670.2; AT5G23670.
GeneID; 832432; -.
Gramene; AT5G23670.1; AT5G23670.1; AT5G23670.
Gramene; AT5G23670.2; AT5G23670.2; AT5G23670.
KEGG; ath:AT5G23670; -.
Araport; AT5G23670; -.
TAIR; locus:2171731; AT5G23670.
eggNOG; KOG1357; Eukaryota.
eggNOG; COG0156; LUCA.
HOGENOM; HOG000206826; -.
InParanoid; Q9LSZ9; -.
KO; K00654; -.
OMA; ISQGQPK; -.
OrthoDB; EOG0936074X; -.
PhylomeDB; Q9LSZ9; -.
BioCyc; ARA:AT5G23670-MONOMER; -.
BioCyc; MetaCyc:AT5G23670-MONOMER; -.
BRENDA; 2.3.1.50; 399.
UniPathway; UPA00222; -.
PRO; PR:Q9LSZ9; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q9LSZ9; baseline and differential.
Genevisible; Q9LSZ9; AT.
GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0016020; C:membrane; IDA:TAIR.
GO; GO:0005773; C:vacuole; IDA:TAIR.
GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
GO; GO:0004758; F:serine C-palmitoyltransferase activity; IDA:TAIR.
GO; GO:0009640; P:photomorphogenesis; IMP:TAIR.
GO; GO:0009555; P:pollen development; IMP:TAIR.
GO; GO:0043067; P:regulation of programmed cell death; IMP:UniProtKB.
GO; GO:0046512; P:sphingosine biosynthetic process; IDA:TAIR.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 1.
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; Apoptosis; 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 2a.
/FTId=PRO_0000419145.
TRANSMEM 2 22 Helical. {ECO:0000255}.
MOD_RES 311 311 N6-(pyridoxal phosphate)lysine.
{ECO:0000250}.
CONFLICT 65 65 D -> N (in Ref. 1 and 2; BAB03231).
{ECO:0000305}.
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


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