SPTC2_RAT
ID SPTC2_RAT Reviewed; 560 AA.
AC Q3B7D2; F1LSV4;
DT 13-FEB-2019, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=Serine palmitoyltransferase 2 {ECO:0000305};
DE EC=2.3.1.50 {ECO:0000250|UniProtKB:O15270};
DE AltName: Full=Long chain base biosynthesis protein 2;
DE Short=LCB 2;
DE AltName: Full=Serine-palmitoyl-CoA transferase 2;
DE Short=SPT 2;
GN Name=Sptlc2 {ECO:0000312|RGD:1305447};
GN Synonyms=Lcb2, Pomt2 {ECO:0000312|RGD:1305447};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP INDUCTION BY MIRNA, AND TISSUE SPECIFICITY.
RX PubMed=21994399; DOI=10.1523/jneurosci.3883-11.2011;
RA Geekiyanage H., Chan C.;
RT "MicroRNA-137/181c regulates serine palmitoyltransferase and in turn
RT amyloid beta, novel targets in sporadic Alzheimer's disease.";
RL J. Neurosci. 31:14820-14830(2011).
CC -!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed
CC with LCB1/SPTLC1 constitutes the catalytic core. The composition of the
CC serine palmitoyltransferase (SPT) complex determines the substrate
CC preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference
CC for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays
CC a preference for C18-CoA substrate (By similarity). Plays an important
CC role in de novo sphyngolipid biosynthesis which is crucial for
CC adipogenesis (By similarity). {ECO:0000250|UniProtKB:O15270,
CC ECO:0000250|UniProtKB:P97363}.
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 Evidence={ECO:0000250|UniProtKB:O15270};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14762;
CC Evidence={ECO:0000250|UniProtKB:O15270};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-serine + octadecanoyl-CoA = 3-oxoeicosasphinganine +
CC CO2 + CoA; Xref=Rhea:RHEA:33683, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:33384, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:57394, ChEBI:CHEBI:65073;
CC Evidence={ECO:0000250|UniProtKB:O15270};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33684;
CC Evidence={ECO:0000250|UniProtKB:O15270};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
CC {ECO:0000250|UniProtKB:O15270}.
CC -!- SUBUNIT: Heterodimer with SPTLC1. Component of the serine
CC palmitoyltransferase (SPT) complex, composed of SPTLC1, either SPTLC2
CC or SPTLC3, and either SPTSSA or SPTSSB. The composition of the complex
CC will define the substrate specificity. {ECO:0000250|UniProtKB:O15270}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000250|UniProtKB:P97363}; Single-pass membrane protein
CC {ECO:0000250|UniProtKB:P97363}.
CC -!- TISSUE SPECIFICITY: Expressed in astrocytes.
CC {ECO:0000269|PubMed:21994399}.
CC -!- INDUCTION: Expression in increased by palmitate at protein level but
CC not mRNA level (PubMed:21994399). Expression is down-regulated by
CC microRNA miR-9, miR29a and miR-29b-1 (at protein level)
CC (PubMed:21994399). {ECO:0000269|PubMed:21994399}.
CC -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; AABR07065137; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC107662; AAI07663.1; -; mRNA.
DR RefSeq; NP_001032174.1; NM_001037097.1.
DR AlphaFoldDB; Q3B7D2; -.
DR SMR; Q3B7D2; -.
DR STRING; 10116.ENSRNOP00000016324; -.
DR jPOST; Q3B7D2; -.
DR GeneID; 366697; -.
DR KEGG; rno:366697; -.
DR UCSC; RGD:1305447; rat.
DR CTD; 9517; -.
DR RGD; 1305447; Sptlc2.
DR eggNOG; KOG1357; Eukaryota.
DR OrthoDB; 438936at2759; -.
DR PhylomeDB; Q3B7D2; -.
DR TreeFam; TF300452; -.
DR BRENDA; 2.3.1.50; 5301.
DR Reactome; R-RNO-1660661; Sphingolipid de novo biosynthesis.
DR UniPathway; UPA00222; -.
DR PRO; PR:Q3B7D2; -.
DR Proteomes; UP000002494; Unplaced.
DR Genevisible; Q3B7D2; RN.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0017059; C:serine C-palmitoyltransferase complex; ISO:RGD.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0004758; F:serine C-palmitoyltransferase activity; ISS:UniProtKB.
DR GO; GO:0060612; P:adipose tissue development; ISS:UniProtKB.
DR GO; GO:0046513; P:ceramide biosynthetic process; ISO:RGD.
DR GO; GO:1904504; P:positive regulation of lipophagy; ISO:RGD.
DR GO; GO:0046511; P:sphinganine biosynthetic process; ISO:RGD.
DR GO; GO:0030148; P:sphingolipid biosynthetic process; ISS:UniProtKB.
DR GO; GO:0006686; P:sphingomyelin biosynthetic process; ISO:RGD.
DR GO; GO:0046512; P:sphingosine biosynthetic process; ISO:RGD.
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 1: Evidence at protein level;
KW Acyltransferase; Endoplasmic reticulum; Lipid metabolism; Membrane;
KW Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
KW Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..560
FT /note="Serine palmitoyltransferase 2"
FT /id="PRO_0000446339"
FT TRANSMEM 65..85
FT /note="Helical"
FT /evidence="ECO:0000255"
FT MOD_RES 377
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT CONFLICT 519..521
FT /note="LDT -> PGE (in Ref. 1; AABR07065137)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 560 AA; 62962 MW; 033420B9173A5400 CRC64;
MRPEPGGCCC RRPMRANGCV KNGEVRNGYL RSSTATIAAA GQIHHITENG GLYKRPFNEA
FEETPMLVAV LTYVGYGVLT LFGYLRDFLR HWRIEKCHHA TEREEQKDFV SLYQDFENFY
TRNLYMRIRD NWNRPICSVP GAKVDIMERQ SHDYNWSFKY TGNIIKGVIN MGSYNYLGFA
RNTGSCQEAA AEVLKTYGAG VCSTRQEIGN LDKHEELEKL VARFLGVEAA LTYGMGFATN
SMNIPALVGK GCLILSDELN HASLVLGARL SGATIRIFKH NNMQSLEKLL KDAIVYGQPR
TRRPWKKILI LVEGIYSMEG SIVRLPEVIA LKKKYKAYLY LDEAHSIGAL GPSGRGVVDY
FGLDPEDVDV MMGTFTKSFG ASGGYIGGKK ELIDYLRTHS HSAVYATSMS PPVMEQIITS
MKCIMGQDGT SLGKECIQQL AENTRYFRRR LKEMGFIIYG NEDSPVVPLM LYMPAKIGAF
GREMLKRNIG VVVVGFPATP IIESRARFCL SAAHTKEILD TALKEIDEVG DLLQLKYSRH
RPLPLLDRPF DETTYEETED
