LCB2B_ORYSJ
ID LCB2B_ORYSJ Reviewed; 499 AA.
AC Q8RYL1; A0A0P0VC95; Q0JGD7;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Long chain base biosynthesis protein 2b;
DE EC=2.3.1.50;
GN OrderedLocusNames=Os01g0928600, LOC_Os01g70360;
GN ORFNames=OsJ_04633, OSJNBa0052O12.11;
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).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RG The rice full-length cDNA consortium;
RT "Oryza sativa full length cDNA.";
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
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=BAF07191.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP004330; BAB90751.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF07191.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014957; BAS76014.1; -; Genomic_DNA.
DR EMBL; CM000138; EAZ14709.1; -; Genomic_DNA.
DR EMBL; AK241034; BAH00934.1; -; mRNA.
DR RefSeq; XP_015613372.1; XM_015757886.1.
DR AlphaFoldDB; Q8RYL1; -.
DR SMR; Q8RYL1; -.
DR STRING; 4530.OS01T0928600-01; -.
DR PaxDb; Q8RYL1; -.
DR PRIDE; Q8RYL1; -.
DR EnsemblPlants; Os01t0928600-01; Os01t0928600-01; Os01g0928600.
DR GeneID; 4326964; -.
DR Gramene; Os01t0928600-01; Os01t0928600-01; Os01g0928600.
DR KEGG; osa:4326964; -.
DR eggNOG; KOG1357; Eukaryota.
DR HOGENOM; CLU_015846_7_0_1; -.
DR InParanoid; Q8RYL1; -.
DR OMA; GTDIGRQ; -.
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 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; Q8RYL1; 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..499
FT /note="Long chain base biosynthesis protein 2b"
FT /id="PRO_0000419151"
FT TRANSMEM 5..25
FT /note="Helical"
FT /evidence="ECO:0000255"
FT MOD_RES 322
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 499 AA; 54484 MW; DE09CFF7BA824CCF CRC64;
MVIKVPYVTA ATTLFSFGLI FGFGHLRDSF RALLRLLFSS AAAADSPAGC NSKGYAPICV
GKEDFYIRRF FRRVQDCFGR PIASKPDAWF DVVERYSTDS NKTLHCTTKT SKCLNLASFN
YLGFAAADEY CTPRVIESLK KYSASTCSSR VDGGNTQLHI ELEELVARFV RKPSAILLAM
GYATNSAIIP ALIGKGGLII SDSLNHNSIV SGARASGATI RVFEHNNPAH LEKLLREQIS
GGQPRTHRAW KKILVIVEGI YSMEGELCKL PEIISVCKKY KVYTYMDEAH SIGAVGKTGR
GVCELLGVDP ADVDIMMGTL SKSFGSSGGY IAASKEIIQH LKLTCPSHIY GTSMSPPAVQ
QVISAMKVIL GEDGTDRGAK KIAQIRDNSN FFRSELQKMG FEVLGDNDSP VMPFMVYNPA
KMPAFSRECL KQNVAVVPVG FPATPLLLGR IRICISASHS REDLIKGLEV ISNVGDLVGI
KYLPVEQEET TSVEKPKKL
