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Serine palmitoyltransferase 3 (EC 2.3.1.50) (Long chain base biosynthesis protein 2b) (LCB2b) (Long chain base biosynthesis protein 3) (LCB 3) (Serine-palmitoyl-CoA transferase 3) (SPT 3)

 SPTC3_HUMAN             Reviewed;         552 AA.
Q9NUV7; A2A2I4; B9EK64; Q05DQ8; Q5T1U4; Q9H1L1; Q9H1Z0;
10-OCT-2002, integrated into UniProtKB/Swiss-Prot.
02-OCT-2007, sequence version 3.
28-FEB-2018, entry version 138.
RecName: Full=Serine palmitoyltransferase 3;
EC=2.3.1.50;
AltName: Full=Long chain base biosynthesis protein 2b;
Short=LCB2b;
AltName: Full=Long chain base biosynthesis protein 3;
Short=LCB 3;
AltName: Full=Serine-palmitoyl-CoA transferase 3;
Short=SPT 3;
Name=SPTLC3; Synonyms=C20orf38, SPTLC2L;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), CATALYTIC ACTIVITY, AND TISSUE
SPECIFICITY.
PubMed=17023427; DOI=10.1074/jbc.M608066200;
Hornemann T., Richard S., Ruetti M.F., Wei Y., von Eckardstein A.;
"Cloning and initial characterization of a new subunit for mammalian
serine-palmitoyltransferase.";
J. Biol. Chem. 281:37275-37281(2006).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
TISSUE=Placenta;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=11780052; DOI=10.1038/414865a;
Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R.,
Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L.,
Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M.,
Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M., Brown A.J.,
Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P.,
Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M.,
Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R.,
Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M.,
Ellington A.G., Frankland J.A., Fraser A., French L., Garner P.,
Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E.,
Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J.,
Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D.,
Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S.,
Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D.,
Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A.,
Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T.,
Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I.,
Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H.,
Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S.,
Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E.,
Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A.,
Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M.,
Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A.,
Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S.,
Rogers J.;
"The DNA sequence and comparative analysis of human chromosome 20.";
Nature 414:865-871(2001).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), AND VARIANT
VAL-140.
TISSUE=Brain, Placenta, and Urinary bladder;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
FUNCTION, CATALYTIC ACTIVITY, AND IDENTIFICATION IN THE SPT COMPLEX.
PubMed=19416851; DOI=10.1073/pnas.0811269106;
Han G., Gupta S.D., Gable K., Niranjanakumari S., Moitra P.,
Eichler F., Brown R.H. Jr., Harmon J.M., Dunn T.M.;
"Identification of small subunits of mammalian serine
palmitoyltransferase that confer distinct acyl-CoA substrate
specificities.";
Proc. Natl. Acad. Sci. U.S.A. 106:8186-8191(2009).
-!- FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer
formed with LCB1/SPTLC1 constitutes the catalytic core. The
composition of the serine palmitoyltransferase (SPT) complex
determines the substrate preference. The SPTLC1-SPTLC3-SPTSSA
isozyme uses both C14-CoA and C16-CoA as substrates, while the
SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of
acyl-CoAs without apparent preference.
{ECO:0000269|PubMed:19416851}.
-!- CATALYTIC ACTIVITY: Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-
sphinganine + CO(2). {ECO:0000269|PubMed:17023427,
ECO:0000269|PubMed:19416851}.
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000250};
-!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
-!- SUBUNIT: Heterodimer with SPTLC1. Component of the serine
palmitoyltransferase (SPT) complex, composed of LCB1/SPTLC1, LCB2
(SPTLC2 or SPTLC3) and ssPT (SPTSSA and SPTSSB).
{ECO:0000269|PubMed:19416851}.
-!- INTERACTION:
O15269:SPTLC1; NbExp=3; IntAct=EBI-11614219, EBI-1044323;
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
{ECO:0000250}; Single-pass membrane protein {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9NUV7-1; Sequence=Displayed;
Name=2;
IsoId=Q9NUV7-2; Sequence=VSP_028167, VSP_028168;
Note=Variant in position: 149:P->A (in dbSNP:rs934335).;
-!- TISSUE SPECIFICITY: Expressed in most tissues, except peripheral
blood cells and bone marrow, with highest levels in heart, kidney,
liver, uterus and skin. {ECO:0000269|PubMed:17023427}.
-!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
aminotransferase family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAH05205.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AK001974; BAA92012.1; -; mRNA.
EMBL; AL133331; CAM13116.1; -; Genomic_DNA.
EMBL; AL050320; CAM13116.1; JOINED; Genomic_DNA.
EMBL; AL109983; CAM13116.1; JOINED; Genomic_DNA.
EMBL; AL445589; CAM13116.1; JOINED; Genomic_DNA.
EMBL; AL445589; CAM16427.1; -; Genomic_DNA.
EMBL; AL050320; CAM16427.1; JOINED; Genomic_DNA.
EMBL; AL109983; CAM16427.1; JOINED; Genomic_DNA.
EMBL; AL133331; CAM16427.1; JOINED; Genomic_DNA.
EMBL; AL050320; CAM27358.1; -; Genomic_DNA.
EMBL; AL109983; CAM27358.1; JOINED; Genomic_DNA.
EMBL; AL133331; CAM27358.1; JOINED; Genomic_DNA.
EMBL; AL445589; CAM27358.1; JOINED; Genomic_DNA.
EMBL; AL109983; CAM28300.1; -; Genomic_DNA.
EMBL; AL050320; CAM28300.1; JOINED; Genomic_DNA.
EMBL; AL133331; CAM28300.1; JOINED; Genomic_DNA.
EMBL; AL445589; CAM28300.1; JOINED; Genomic_DNA.
EMBL; BC005205; AAH05205.1; ALT_SEQ; mRNA.
EMBL; BC020656; AAH20656.1; -; mRNA.
EMBL; BC150644; AAI50645.1; -; mRNA.
CCDS; CCDS13115.2; -. [Q9NUV7-1]
RefSeq; NP_060797.2; NM_018327.2. [Q9NUV7-1]
UniGene; Hs.425023; -.
ProteinModelPortal; Q9NUV7; -.
SMR; Q9NUV7; -.
CORUM; Q9NUV7; -.
DIP; DIP-60753N; -.
IntAct; Q9NUV7; 4.
STRING; 9606.ENSP00000381968; -.
DrugBank; DB00114; Pyridoxal Phosphate.
SwissLipids; SLP:000000153; -.
iPTMnet; Q9NUV7; -.
PhosphoSitePlus; Q9NUV7; -.
SwissPalm; Q9NUV7; -.
BioMuta; SPTLC3; -.
DMDM; 158931158; -.
EPD; Q9NUV7; -.
MaxQB; Q9NUV7; -.
PaxDb; Q9NUV7; -.
PeptideAtlas; Q9NUV7; -.
PRIDE; Q9NUV7; -.
Ensembl; ENST00000399002; ENSP00000381968; ENSG00000172296. [Q9NUV7-1]
GeneID; 55304; -.
KEGG; hsa:55304; -.
UCSC; uc002wod.2; human. [Q9NUV7-1]
CTD; 55304; -.
DisGeNET; 55304; -.
EuPathDB; HostDB:ENSG00000172296.12; -.
GeneCards; SPTLC3; -.
H-InvDB; HIX0019548; -.
HGNC; HGNC:16253; SPTLC3.
HPA; HPA044247; -.
HPA; HPA048079; -.
MIM; 611120; gene.
neXtProt; NX_Q9NUV7; -.
OpenTargets; ENSG00000172296; -.
PharmGKB; PA162404677; -.
eggNOG; KOG1357; Eukaryota.
eggNOG; COG0156; LUCA.
GeneTree; ENSGT00550000074678; -.
HOVERGEN; HBG002230; -.
InParanoid; Q9NUV7; -.
KO; K00654; -.
OMA; IDDAHAV; -.
OrthoDB; EOG091G0558; -.
PhylomeDB; Q9NUV7; -.
TreeFam; TF300452; -.
BioCyc; MetaCyc:HS16070-MONOMER; -.
BRENDA; 2.3.1.50; 2681.
Reactome; R-HSA-1660661; Sphingolipid de novo biosynthesis.
UniPathway; UPA00222; -.
ChiTaRS; SPTLC3; human.
GenomeRNAi; 55304; -.
PRO; PR:Q9NUV7; -.
Proteomes; UP000005640; Chromosome 20.
Bgee; ENSG00000172296; -.
CleanEx; HS_SPTLC3; -.
ExpressionAtlas; Q9NUV7; baseline and differential.
Genevisible; Q9NUV7; HS.
GO; GO:0005789; C:endoplasmic reticulum membrane; TAS:Reactome.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0017059; C:serine C-palmitoyltransferase complex; IDA:UniProtKB.
GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
GO; GO:0004758; F:serine C-palmitoyltransferase activity; IDA:UniProtKB.
GO; GO:0046520; P:sphingoid biosynthetic process; IDA:MGI.
GO; GO:0030148; P:sphingolipid biosynthetic process; TAS:UniProtKB.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 2.
InterPro; IPR001917; Aminotrans_II_pyridoxalP_BS.
InterPro; IPR004839; Aminotransferase_I/II.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
Pfam; PF00155; Aminotran_1_2; 1.
SUPFAM; SSF53383; SSF53383; 1.
PROSITE; PS00599; AA_TRANSFER_CLASS_2; 1.
1: Evidence at protein level;
Acyltransferase; Alternative splicing; Complete proteome;
Endoplasmic reticulum; Lipid metabolism; Membrane; Polymorphism;
Pyridoxal phosphate; Reference proteome; Sphingolipid metabolism;
Transferase; Transmembrane; Transmembrane helix.
CHAIN 1 552 Serine palmitoyltransferase 3.
/FTId=PRO_0000079426.
TRANSMEM 59 79 Helical. {ECO:0000255}.
MOD_RES 371 371 N6-(pyridoxal phosphate)lysine.
{ECO:0000250}.
VAR_SEQ 102 175 DFVPLYQDFENFYTRNLYMRIRDNWNRPICSAPGPLFDLME
RVSDDYNWTFRFTGRVIKDVINMGSYNFLGLAA -> VRMR
TSLDLCQCLLLSKVFSEVVMQVQILESMRCSGTIQGKFHSS
PPPKPHYPWAYGPVFTNISWATTICHIPN (in isoform
2). {ECO:0000303|PubMed:14702039,
ECO:0000303|PubMed:15489334}.
/FTId=VSP_028167.
VAR_SEQ 176 552 Missing (in isoform 2).
{ECO:0000303|PubMed:14702039,
ECO:0000303|PubMed:15489334}.
/FTId=VSP_028168.
VARIANT 140 140 L -> V (in dbSNP:rs243887).
{ECO:0000269|PubMed:15489334}.
/FTId=VAR_048230.
SEQUENCE 552 AA; 62049 MW; EED341220DCA683A CRC64;
MANPGGGAVC NGKLHNHKKQ SNGSQSRNCT KNGIVKEAQQ NGKPHFYDKL IVESFEEAPL
HVMVFTYMGY GIGTLFGYLR DFLRNWGIEK CNAAVERKEQ KDFVPLYQDF ENFYTRNLYM
RIRDNWNRPI CSAPGPLFDL MERVSDDYNW TFRFTGRVIK DVINMGSYNF LGLAAKYDES
MRTIKDVLEV YGTGVASTRH EMGTLDKHKE LEDLVAKFLN VEAAMVFGMG FATNSMNIPA
LVGKGCLILS DELNHTSLVL GARLSGATIR IFKHNNTQSL EKLLRDAVIY GQPRTRRAWK
KILILVEGVY SMEGSIVHLP QIIALKKKYK AYLYIDEAHS IGAVGPTGRG VTEFFGLDPH
EVDVLMGTFT KSFGASGGYI AGRKDLVDYL RVHSHSAVYA SSMSPPIAEQ IIRSLKLIMG
LDGTTQGLQR VQQLAKNTRY FRQRLQEMGF IIYGNENASV VPLLLYMPGK VAAFARHMLE
KKIGVVVVGF PATPLAEARA RFCVSAAHTR EMLDTVLEAL DEMGDLLQLK YSRHKKSARP
ELYDETSFEL ED


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