ID   SGPL_ORYSJ              Reviewed;         539 AA.
AC   Q52RG7; B7FAK6; Q0JRH4; Q655L2; Q7F2G0;
DT   25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT   11-MAY-2016, sequence version 3.
DT   03-AUG-2022, entry version 107.
DE   RecName: Full=Sphingosine-1-phosphate lyase;
DE            Short=S1PL;
DE            Short=SP-lyase;
DE            Short=SPL;
DE            EC=4.1.2.27;
DE   AltName: Full=Sphingosine-1-phosphate aldolase;
DE   Flags: Precursor;
GN   Name=SPL; OrderedLocusNames=Os01g0100900, LOC_Os01g01080;
GN   ORFNames=OsJ_00009 {ECO:0000312|EMBL:EEE53694.1}, P0402A09.4, P0672D08.8;
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 [MRNA].
RC   STRAIN=cv. Nipponbare;
RA   Niu Y., Wang J., Liu K., Wang D.;
RT   "Molecular and functional analysis of putative sphingosine-1-phosphate
RT   lyases from Arabidopsis thaliana and rice.";
RL   Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN   [2]
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   [3]
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   [4]
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   [5]
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   [6]
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   [7]
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: Cleaves phosphorylated sphingoid bases (PSBs), such as
CC       sphingosine-1-phosphate, into fatty aldehydes and phosphoethanolamine.
CC       Elevates stress-induced ceramide production and apoptosis (By
CC       similarity). {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=sphinganine 1-phosphate = hexadecanal + phosphoethanolamine;
CC         Xref=Rhea:RHEA:18593, ChEBI:CHEBI:17600, ChEBI:CHEBI:57939,
CC         ChEBI:CHEBI:58190; EC=4.1.2.27;
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000250};
CC   -!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
CC   -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane {ECO:0000250};
CC       Single-pass type III membrane protein {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the group II decarboxylase family. Sphingosine-
CC       1-phosphate lyase subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB62623.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD45497.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AY972084; AAX89367.1; -; mRNA.
DR   EMBL; AP003610; BAB62623.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP003727; BAD45497.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008207; BAF03654.2; -; Genomic_DNA.
DR   EMBL; AP014957; BAS69918.1; -; Genomic_DNA.
DR   EMBL; CM000138; EEE53694.1; -; Genomic_DNA.
DR   EMBL; AK243573; BAH01654.1; -; mRNA.
DR   RefSeq; XP_015621818.1; XM_015766332.1.
DR   AlphaFoldDB; Q52RG7; -.
DR   SMR; Q52RG7; -.
DR   STRING; 4530.OS01T0100900-01; -.
DR   PaxDb; Q52RG7; -.
DR   PRIDE; Q52RG7; -.
DR   EnsemblPlants; Os01t0100900-01; Os01t0100900-01; Os01g0100900.
DR   GeneID; 4326459; -.
DR   Gramene; Os01t0100900-01; Os01t0100900-01; Os01g0100900.
DR   KEGG; osa:4326459; -.
DR   eggNOG; KOG1383; Eukaryota.
DR   InParanoid; Q52RG7; -.
DR   OMA; FKDHQFT; -.
DR   OrthoDB; 517323at2759; -.
DR   PlantReactome; R-OSA-1119325; Sphingolipid metabolism.
DR   UniPathway; UPA00222; -.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000007752; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
DR   Genevisible; Q52RG7; 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:0008117; F:sphinganine-1-phosphate aldolase activity; IBA:GO_Central.
DR   GO; GO:0019752; P:carboxylic acid metabolic process; IEA:InterPro.
DR   GO; GO:0030149; P:sphingolipid catabolic process; IBA:GO_Central.
DR   Gene3D; 3.40.640.10; -; 1.
DR   Gene3D; 3.90.1150.10; -; 1.
DR   InterPro; IPR002129; PyrdxlP-dep_de-COase.
DR   InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR   InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR   InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR   Pfam; PF00282; Pyridoxal_deC; 1.
DR   SUPFAM; SSF53383; SSF53383; 1.
PE   2: Evidence at transcript level;
KW   Apoptosis; Endoplasmic reticulum; Lipid metabolism; Lyase; Membrane;
KW   Pyridoxal phosphate; Reference proteome; Signal; Signal-anchor;
KW   Sphingolipid metabolism; Transmembrane; Transmembrane helix.
FT   SIGNAL          1..46
FT                   /evidence="ECO:0000255"
FT   CHAIN           47..539
FT                   /note="Sphingosine-1-phosphate lyase"
FT                   /id="PRO_0000247464"
FT   TOPO_DOM        47..54
FT                   /note="Lumenal"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        55..75
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TOPO_DOM        76..539
FT                   /note="Cytoplasmic"
FT                   /evidence="ECO:0000255"
FT   MOD_RES         344
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   539 AA;  58272 MW;  74D809622A81342E CRC64;
     MELAMDFALR LRDAANHHLS RYEPLVLLAA PLLALLAART LHAAAAAVAD RGLRTVLLAL
     AMTAIKLLPG VSAYINAEKR KVVDQLQSGG TSTKSTLRTE LPTVGLSNQV INDLETLKAR
     DVNWQGKCSG TVYIAGSESE GHFALINKAY SMFSHTNPLH QDVFKSVAQL EAEVVAMTAA
     LLGIKEKSSG GQICGNMTSG GTESILLAVK TSRDYMRTKK GITKPEMIIA ESAHSAYDKA
     AQYFNIKVRR VPVNKEFLAD VKGFKRCING NTIMMVGSAP GFPHGLIDPI EELGELASRY
     DICLHVDLCL GGFVLPFARK LGYPIPPFDF CVKGVTSIST DVHKYGLAPK GTSIVLYKNH
     EIRKHQFVAV TEWTGGLYVS PTIAGSRPGG LIAGAWAAMT SLGLNGYMEN TGHIMEVSKK
     IQRGIEDIPG LFVIGKPDMT VVAFGSDSVD IFEVNDIMSS KGWHLNALQR PNSLHICVTL
     QHTVIYEEFL KDLKDSVDTV KANPGPISGG RAPIYGAAGK MPDRGMVREL LVEFMDASC