ID   LCB2A_ORYSJ             Reviewed;         488 AA.
AC   Q2R3K3; A0A0P0Y2M2; B9GAX0;
DT   03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT   24-JAN-2006, sequence version 1.
DT   27-MAR-2024, entry version 120.
DE   RecName: Full=Long chain base biosynthesis protein 2a;
DE            EC=2.3.1.50;
GN   OrderedLocusNames=Os11g0516000, LOC_Os11g31640; ORFNames=OsJ_34042;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG   The rice chromosomes 11 and 12 sequencing consortia;
RT   "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT   genes and recent gene duplications.";
RL   BMC Biol. 3:20-20(2005).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
CC   -!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed
CC       with LCB1 constitutes the catalytic core (By similarity).
CC       {ECO:0000250}.
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 LCB1. Component of the serine
CC       palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (By
CC       similarity). {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane {ECO:0000250};
CC       Single-pass membrane protein {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC       aminotransferase family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=EEE52176.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; DP000010; ABA93932.1; -; Genomic_DNA.
DR   EMBL; AP008217; BAF28335.1; -; Genomic_DNA.
DR   EMBL; AP014967; BAT14191.1; -; Genomic_DNA.
DR   EMBL; CM000148; EEE52176.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AK069007; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015617901.1; XM_015762415.1.
DR   AlphaFoldDB; Q2R3K3; -.
DR   SMR; Q2R3K3; -.
DR   STRING; 39947.Q2R3K3; -.
DR   PaxDb; 39947-Q2R3K3; -.
DR   EnsemblPlants; Os11t0516000-01; Os11t0516000-01; Os11g0516000.
DR   GeneID; 4350591; -.
DR   Gramene; Os11t0516000-01; Os11t0516000-01; Os11g0516000.
DR   KEGG; osa:4350591; -.
DR   eggNOG; KOG1357; Eukaryota.
DR   HOGENOM; CLU_015846_7_0_1; -.
DR   InParanoid; Q2R3K3; -.
DR   OMA; FCVSNHP; -.
DR   OrthoDB; 9643at2759; -.
DR   PlantReactome; R-OSA-1119325; Sphingolipid metabolism.
DR   PlantReactome; R-OSA-1119610; Biotin biosynthesis II.
DR   UniPathway; UPA00222; -.
DR   Proteomes; UP000000763; Chromosome 11.
DR   Proteomes; UP000007752; Chromosome 11.
DR   Proteomes; UP000059680; Chromosome 11.
DR   GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
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; IBA:GO_Central.
DR   GO; GO:0046513; P:ceramide biosynthetic process; IBA:GO_Central.
DR   GO; GO:0046512; P:sphingosine biosynthetic process; IBA:GO_Central.
DR   CDD; cd06454; KBL_like; 1.
DR   Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR   Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 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   PANTHER; PTHR13693; CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE; 1.
DR   PANTHER; PTHR13693:SF104; LONG CHAIN BASE BIOSYNTHESIS PROTEIN 2A; 1.
DR   Pfam; PF00155; Aminotran_1_2; 1.
DR   SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR   PROSITE; PS00599; AA_TRANSFER_CLASS_2; 1.
DR   Genevisible; Q2R3K3; OS.
PE   2: Evidence at transcript level;
KW   Acyltransferase; Endoplasmic reticulum; Lipid metabolism; Membrane;
KW   Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
KW   Transferase; Transmembrane; Transmembrane helix.
FT   CHAIN           1..488
FT                   /note="Long chain base biosynthesis protein 2a"
FT                   /id="PRO_0000419150"
FT   TRANSMEM        4..24
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   MOD_RES         311
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        289
FT                   /note="R -> W (in Ref. 6; AK069007)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   488 AA;  53690 MW;  E4478AE71F6F8373 CRC64;
     MVRLPYTTAL TTLFSYGLLF AFGQLRDFFR KLIDWFKAKN VKGYAPICLG LEDFYVRRLY
     LRIQDCFGRP IASAPDAWFD VVERYSNDSN KTLKRTSNTT RCLNLGSYNY LGFAAADEYC
     TPLVIESLKK YSPSTCSVRV DGGTTKLHTE LEELVARFVG KPAAILFGMG YVTNSAIIPC
     LVGKGGLIIS DSLNHNSIVN GARGSGATVR VFQHNSPAHL EEVLREQIAG GQPRTHRPWK
     KIIVIVEGIY SMEGELCKLP EIIAVCKKYK AYTYLDEAHS IGAVGQSGRG VCELLGVDPA
     DVDIMMGTFT KSFGSCGGYI AASKEIIQHL KLSCPAHIYA TSMSPPAVQQ VISAIKVILG
     EDGSNRGAQK LARIRENSNF FRSELKKMGF EVLGDNDSPV MPIMLYNPAK IPAFSRECLR
     QKVAVVTVAF PATPLLLARA RICISASHTR EDLIKALDVI SRVGDLVGIK YFPAEPPKIA
     EADHDKLE
//