LCB2A_ORYSJ
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 03-AUG-2022, entry version 113.
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; 4530.OS11T0516000-01; -.
DR PaxDb; Q2R3K3; -.
DR PRIDE; 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; IEDEPPY; -.
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 11.
DR Proteomes; UP000007752; Chromosome 11.
DR Proteomes; UP000059680; Chromosome 11.
DR Genevisible; Q2R3K3; OS.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
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 Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 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 Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00599; AA_TRANSFER_CLASS_2; 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..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
