ID   LCB1C_ORYSJ             Reviewed;         482 AA.
AC   Q7G4P2; A0A0P0XTG3; B9G7U8; Q53QX1;
DT   03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 2.
DT   03-AUG-2022, entry version 110.
DE   RecName: Full=Long chain base biosynthesis protein 1c;
DE            EC=2.3.1.50;
GN   OrderedLocusNames=Os10g0189600, LOC_Os10g11200;
GN   ORFNames=OsJ_30932, OSJNBa0079H13;
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=12791992; DOI=10.1126/science.1083523;
RA   Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA   Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA   Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA   Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA   Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA   Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA   Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA   Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA   Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA   Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA   Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA   Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA   Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA   Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA   Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA   Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA   Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT   "In-depth view of structure, activity, and evolution of rice chromosome
RT   10.";
RL   Science 300:1566-1569(2003).
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 LCB2 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 LCB2. 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=AAX95555.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=EEE50683.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AC104616; AAX95555.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; DP000086; AAP52538.2; -; Genomic_DNA.
DR   EMBL; AP008216; BAF26186.1; -; Genomic_DNA.
DR   EMBL; AP014966; BAT10181.1; -; Genomic_DNA.
DR   EMBL; CM000147; EEE50683.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AK100991; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015612907.1; XM_015757421.1.
DR   AlphaFoldDB; Q7G4P2; -.
DR   SMR; Q7G4P2; -.
DR   STRING; 4530.OS10T0189600-02; -.
DR   PaxDb; Q7G4P2; -.
DR   PRIDE; Q7G4P2; -.
DR   EnsemblPlants; Os10t0189600-01; Os10t0189600-01; Os10g0189600.
DR   EnsemblPlants; Os10t0189600-02; Os10t0189600-02; Os10g0189600.
DR   GeneID; 4348231; -.
DR   Gramene; Os10t0189600-01; Os10t0189600-01; Os10g0189600.
DR   Gramene; Os10t0189600-02; Os10t0189600-02; Os10g0189600.
DR   KEGG; osa:4348231; -.
DR   eggNOG; KOG1358; Eukaryota.
DR   HOGENOM; CLU_015846_0_1_1; -.
DR   InParanoid; Q7G4P2; -.
DR   OMA; MMEMVLP; -.
DR   OrthoDB; 438936at2759; -.
DR   PlantReactome; R-OSA-1119325; Sphingolipid metabolism.
DR   PlantReactome; R-OSA-1119610; Biotin biosynthesis II.
DR   UniPathway; UPA00222; -.
DR   Proteomes; UP000000763; Chromosome 10.
DR   Proteomes; UP000007752; Chromosome 10.
DR   Proteomes; UP000059680; Chromosome 10.
DR   Genevisible; Q7G4P2; OS.
DR   GO; GO:0005783; C:endoplasmic reticulum; IBA:GO_Central.
DR   GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
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   Gene3D; 3.40.640.10; -; 1.
DR   Gene3D; 3.90.1150.10; -; 1.
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.
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..482
FT                   /note="Long chain base biosynthesis protein 1c"
FT                   /id="PRO_0000419149"
FT   TRANSMEM        33..53
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   CONFLICT        157
FT                   /note="D -> N (in Ref. 6; AK100991)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   482 AA;  51995 MW;  BC5AB3DFACF2D8F3 CRC64;
     MMEMVLPVAN ATAAALARVS AVFNAPLARA VVFGIHIDGH LVVEGLLIAA ILFQLSRKSY
     KPPKKPLTER EVDELCDDWQ PEPLCPPIKE GARIDTPTLE SAAGPHTTVD GKEVVNFASA
     NYLGLIGNEK IIDSCVGSVE KYGVGSCGPR SFYGTIDVHL DCESKIANFL GTQDSILYSY
     GISTIFSVIP AFCKKGDIIV ADEGVHWAVQ NGLQLSRSTV VYFKHNDMAS LASILEKLTH
     GNKHTEKIRR YIVVEAIYQN SGQIAPLDEI VRLKEKYRFR VILEESHSFG VLGKSGRGLA
     EHYGVPVEKI DIITAGMGNA LATDGGFCTG SVRVVDHQRL SSSGYVFSAS LPPYLASAAM
     SAVNHLEENP SVLANLRSNI ALLHKELSDI PGLEIASNIL SPIVFLKLKT PTGSAVADLE
     LLEIIAEKVL MEDSVFIAAT KRSSLDKCRL PVGIRLFVSA GHTESDIFKV SASLKRVAAS
     VV