ID   LCB2C_ORYSJ             Reviewed;         497 AA.
AC   Q8RYL0; A0A0P0VCB1;
DT   03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   27-MAR-2024, entry version 134.
DE   RecName: Full=Long chain base biosynthesis protein 2c;
DE            EC=2.3.1.50;
GN   OrderedLocusNames=Os01g0928700, LOC_Os01g70370;
GN   ORFNames=OsJ_04634, OSJNBa0052O12.13;
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=12447438; DOI=10.1038/nature01184;
RA   Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA   Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA   Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA   Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA   Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA   Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA   Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA   Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA   Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA   Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA   Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA   Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA   Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT   "The genome sequence and structure of rice chromosome 1.";
RL   Nature 420:312-316(2002).
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).
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}.
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DR   EMBL; AP004330; BAB90752.1; -; Genomic_DNA.
DR   EMBL; AP008207; BAF07192.1; -; Genomic_DNA.
DR   EMBL; AP014957; BAS76015.1; -; Genomic_DNA.
DR   EMBL; CM000138; EAZ14710.1; -; Genomic_DNA.
DR   RefSeq; XP_015613384.1; XM_015757898.1.
DR   AlphaFoldDB; Q8RYL0; -.
DR   SMR; Q8RYL0; -.
DR   STRING; 39947.Q8RYL0; -.
DR   PaxDb; 39947-Q8RYL0; -.
DR   EnsemblPlants; Os01t0928700-00; Os01t0928700-00; Os01g0928700.
DR   GeneID; 4326965; -.
DR   Gramene; Os01t0928700-00; Os01t0928700-00; Os01g0928700.
DR   KEGG; osa:4326965; -.
DR   eggNOG; KOG1357; Eukaryota.
DR   HOGENOM; CLU_015846_7_0_1; -.
DR   InParanoid; Q8RYL0; -.
DR   OMA; YAEPMSV; -.
DR   OrthoDB; 341090at2759; -.
DR   PlantReactome; R-OSA-1119325; Sphingolipid metabolism.
DR   PlantReactome; R-OSA-1119610; Biotin biosynthesis II.
DR   UniPathway; UPA00222; -.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000007752; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
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:SF3; LD36009P; 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; Q8RYL0; OS.
PE   3: Inferred from homology;
KW   Acyltransferase; Endoplasmic reticulum; Lipid metabolism; Membrane;
KW   Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
KW   Transferase; Transmembrane; Transmembrane helix.
FT   CHAIN           1..497
FT                   /note="Long chain base biosynthesis protein 2c"
FT                   /id="PRO_0000419152"
FT   TRANSMEM        4..24
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   MOD_RES         319
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   497 AA;  54647 MW;  7EF5833AA6538DB5 CRC64;
     MVRVPFVTAV TTVFSYGVIF GFGHLRDWFR ALLRSLFSGH SPAAAGTNLK GYAPICGGQE
     DFYYRRFVRR VQDCFWRPIA SKPDAWFDVV ERYSNDSNKT LHRTTKTSRC LNLGSYNYLG
     FAAADEYCTP RVIESLKKYS ASTCSVRVDG GNTKLHVELE ELVARFVGKP AAILFGMGYV
     TNSAIIPALI GKGGLIISDS LNHNSIVNGA RGSGASVQVF QHNNPAHLEE VLREQIAGGQ
     PRTHRRWKKI IVIVEGIYSM EGELCKLPEI VAVCKKYKAY TYLDEAHSIG AVGKTGRGVC
     ELLGVDPADV DIMMGTFTKS FGSCGGYIAA SKEIIDHLKH ICPAHIYATS MSPPAVQQVI
     SAIEVILGED GSDRGAKKLA QIRENSNFFR SELEKMGFEV LGDNDSPVMP IMLYNPAKMP
     AFSRECLRQK VAIVTVSFPA TPLLLARARI CISASHSRED LIKGLEVISK VGDLVGIKYL
     PVEHEKTTSA EKLKKIQ
//