ID   LCB1A_ORYSJ             Reviewed;         485 AA.
AC   Q10P01; A0A0P0VVJ5; Q10P00; Q10P02;
DT   03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   25-MAY-2022, entry version 100.
DE   RecName: Full=Long chain base biosynthesis protein 1a;
DE            EC=2.3.1.50;
GN   OrderedLocusNames=Os03g0252800, LOC_Os03g14800; ORFNames=OsJ_10166;
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=16109971; DOI=10.1101/gr.3869505;
RG   The rice chromosome 3 sequencing consortium;
RA   Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA   Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA   Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA   Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA   Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA   Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA   Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA   Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA   Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA   Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA   O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA   Jin W., Lee H.R., Jiang J., Jackson S.;
RT   "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT   and diverged grass species.";
RL   Genome Res. 15:1284-1291(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 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=ABF95003.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=ABF95004.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=ABF95005.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; DP000009; ABF95002.1; -; Genomic_DNA.
DR   EMBL; DP000009; ABF95003.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; DP000009; ABF95004.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; DP000009; ABF95005.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008209; BAF11490.1; -; Genomic_DNA.
DR   EMBL; AP014959; BAS83299.1; -; Genomic_DNA.
DR   EMBL; CM000140; EAZ26297.1; -; Genomic_DNA.
DR   EMBL; AK065537; BAG89556.1; -; mRNA.
DR   EMBL; AK067765; BAG90585.1; -; mRNA.
DR   RefSeq; XP_015633205.1; XM_015777719.1.
DR   RefSeq; XP_015633207.1; XM_015777721.1.
DR   RefSeq; XP_015633208.1; XM_015777722.1.
DR   AlphaFoldDB; Q10P01; -.
DR   SMR; Q10P01; -.
DR   STRING; 4530.OS03T0252800-01; -.
DR   PaxDb; Q10P01; -.
DR   PRIDE; Q10P01; -.
DR   EnsemblPlants; Os03t0252800-01; Os03t0252800-01; Os03g0252800.
DR   GeneID; 4332274; -.
DR   Gramene; Os03t0252800-01; Os03t0252800-01; Os03g0252800.
DR   KEGG; osa:4332274; -.
DR   eggNOG; KOG1358; Eukaryota.
DR   HOGENOM; CLU_015846_0_1_1; -.
DR   InParanoid; Q10P01; -.
DR   OMA; RNTPTFA; -.
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 3.
DR   Proteomes; UP000007752; Chromosome 3.
DR   Proteomes; UP000059680; Chromosome 3.
DR   Genevisible; Q10P01; 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..485
FT                   /note="Long chain base biosynthesis protein 1a"
FT                   /id="PRO_0000419147"
FT   TRANSMEM        32..52
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   485 AA;  52426 MW;  CC3E17D2310E76CF CRC64;
     MDMALPIVNA TAAVLARVSA AFNAPFARAV VFGVHIDGHL VVEGLLIAVI VFQLSRKSYK
     PPKKPLSEKE IDELCDEWEP EPLCPPIKDG ARIDTPMLES AAAPHTTIDG KEVINFASAN
     YLGLIGNEKI IDSCVGSLEK YGVGSCGPRG FYGTIDVHLD CEAKIAKFLG TPDSILYSYG
     ISTIFSVIPA FCKKGDIIVA DEGVHWAVQN GLHLSRSTVV YFKHNDMASL ANTLEKLTRG
     NKRAEKIRRY IVVESIYQNS GQIAPLDEIV RLKEKYRFRV ILEESHSFGV LGQSGRGLAE
     HYGVPIDKID IITAGMGNAL ATDGGFCTGS VRVVDHQRLS SSGYVFSASL PPYLASAAVS
     AVSYLEGNPS VLADLRSNIS FLHKELSGTP GLEISSHVLS PIVFLKLKKS TGSSNTDIDL
     LETIAERVLK EDSVFIVASK RSPLDRCKLP VGIRLFMSAG HTDSDISKVS SSLKRVSASV
     LSDYI