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Protein

Serine palmitoyltransferase 3

Gene

SPTLC3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.2 Publications

Cofactori

Pathway:isphingolipid metabolism

This protein is involved in the pathway sphingolipid metabolism, which is part of Lipid metabolism.
View all proteins of this organism that are known to be involved in the pathway sphingolipid metabolism and in Lipid metabolism.

GO - Molecular functioni

  • pyridoxal phosphate binding Source: InterPro
  • serine C-palmitoyltransferase activity Source: UniProtKB

GO - Biological processi

  • small molecule metabolic process Source: Reactome
  • sphingoid biosynthetic process Source: MGI
  • sphingolipid biosynthetic process Source: UniProtKB
  • sphingolipid metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Lipid metabolism, Sphingolipid metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc:HS16070-MONOMER.
BRENDAi2.3.1.50. 2681.
ReactomeiREACT_115810. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine palmitoyltransferase 3 (EC:2.3.1.50)
Alternative name(s):
Long chain base biosynthesis protein 2b
Short name:
LCB2b
Long chain base biosynthesis protein 3
Short name:
LCB 3
Serine-palmitoyl-CoA transferase 3
Short name:
SPT 3
Gene namesi
Name:SPTLC3
Synonyms:C20orf38, SPTLC2L
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:16253. SPTLC3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei59 – 7921HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162404677.

Polymorphism and mutation databases

BioMutaiSPTLC3.
DMDMi158931158.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 552552Serine palmitoyltransferase 3PRO_0000079426Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei371 – 3711N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

MaxQBiQ9NUV7.
PaxDbiQ9NUV7.
PRIDEiQ9NUV7.

PTM databases

PhosphoSiteiQ9NUV7.

Expressioni

Tissue specificityi

Expressed in most tissues, except peripheral blood cells and bone marrow, with highest levels in heart, kidney, liver, uterus and skin.1 Publication

Gene expression databases

BgeeiQ9NUV7.
CleanExiHS_SPTLC3.
ExpressionAtlasiQ9NUV7. baseline and differential.
GenevisibleiQ9NUV7. HS.

Organism-specific databases

HPAiHPA044247.

Interactioni

Subunit structurei

Heterodimer with SPTLC1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1/SPTLC1, LCB2 (SPTLC2 or SPTLC3) and ssPT (SPTSSA and SPTSSB).1 Publication

Protein-protein interaction databases

DIPiDIP-60753N.
STRINGi9606.ENSP00000381968.

Structurei

3D structure databases

ProteinModelPortaliQ9NUV7.
SMRiQ9NUV7. Positions 162-527.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
GeneTreeiENSGT00550000074678.
HOVERGENiHBG002230.
InParanoidiQ9NUV7.
KOiK00654.
OMAiNGNLHNH.
OrthoDBiEOG73RBB0.
PhylomeDBiQ9NUV7.
TreeFamiTF300452.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NUV7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MANPGGGAVC NGKLHNHKKQ SNGSQSRNCT KNGIVKEAQQ NGKPHFYDKL
60 70 80 90 100
IVESFEEAPL HVMVFTYMGY GIGTLFGYLR DFLRNWGIEK CNAAVERKEQ
110 120 130 140 150
KDFVPLYQDF ENFYTRNLYM RIRDNWNRPI CSAPGPLFDL MERVSDDYNW
160 170 180 190 200
TFRFTGRVIK DVINMGSYNF LGLAAKYDES MRTIKDVLEV YGTGVASTRH
210 220 230 240 250
EMGTLDKHKE LEDLVAKFLN VEAAMVFGMG FATNSMNIPA LVGKGCLILS
260 270 280 290 300
DELNHTSLVL GARLSGATIR IFKHNNTQSL EKLLRDAVIY GQPRTRRAWK
310 320 330 340 350
KILILVEGVY SMEGSIVHLP QIIALKKKYK AYLYIDEAHS IGAVGPTGRG
360 370 380 390 400
VTEFFGLDPH EVDVLMGTFT KSFGASGGYI AGRKDLVDYL RVHSHSAVYA
410 420 430 440 450
SSMSPPIAEQ IIRSLKLIMG LDGTTQGLQR VQQLAKNTRY FRQRLQEMGF
460 470 480 490 500
IIYGNENASV VPLLLYMPGK VAAFARHMLE KKIGVVVVGF PATPLAEARA
510 520 530 540 550
RFCVSAAHTR EMLDTVLEAL DEMGDLLQLK YSRHKKSARP ELYDETSFEL

ED
Length:552
Mass (Da):62,049
Last modified:October 2, 2007 - v3
Checksum:iEED341220DCA683A
GO
Isoform 2 (identifier: Q9NUV7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     102-175: DFVPLYQDFE...GSYNFLGLAA → VRMRTSLDLC...WATTICHIPN
     176-552: Missing.

Show »
Length:175
Mass (Da):19,693
Checksum:i0B52D6020D5F73F3
GO

Sequence cautioni

The sequence AAH05205.1 differs from that shown.Contaminating sequence. Potential poly-A sequence.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti140 – 1401L → V.1 Publication
Corresponds to variant rs243887 [ dbSNP | Ensembl ].
VAR_048230
Isoform 2 (identifier: Q9NUV7-2)
Natural varianti149 – 1491P → A.
Corresponds to variant rs934335 [ dbSNP | Ensembl ].

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei102 – 17574DFVPL…LGLAA → VRMRTSLDLCQCLLLSKVFS EVVMQVQILESMRCSGTIQG KFHSSPPPKPHYPWAYGPVF TNISWATTICHIPN in isoform 2. 2 PublicationsVSP_028167Add
BLAST
Alternative sequencei176 – 552377Missing in isoform 2. 2 PublicationsVSP_028168Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001974 mRNA. Translation: BAA92012.1.
AL133331
, AL050320, AL109983, AL445589 Genomic DNA. Translation: CAM13116.1.
AL445589
, AL050320, AL109983, AL133331 Genomic DNA. Translation: CAM16427.1.
AL050320
, AL109983, AL133331, AL445589 Genomic DNA. Translation: CAM27358.1.
AL109983
, AL050320, AL133331, AL445589 Genomic DNA. Translation: CAM28300.1.
BC005205 mRNA. Translation: AAH05205.1. Sequence problems.
BC020656 mRNA. Translation: AAH20656.1.
BC150644 mRNA. Translation: AAI50645.1.
CCDSiCCDS13115.2. [Q9NUV7-1]
RefSeqiNP_060797.2. NM_018327.2. [Q9NUV7-1]
UniGeneiHs.425023.

Genome annotation databases

EnsembliENST00000399002; ENSP00000381968; ENSG00000172296.
GeneIDi55304.
KEGGihsa:55304.
UCSCiuc002woc.3. human. [Q9NUV7-2]
uc002wod.1. human. [Q9NUV7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001974 mRNA. Translation: BAA92012.1.
AL133331
, AL050320, AL109983, AL445589 Genomic DNA. Translation: CAM13116.1.
AL445589
, AL050320, AL109983, AL133331 Genomic DNA. Translation: CAM16427.1.
AL050320
, AL109983, AL133331, AL445589 Genomic DNA. Translation: CAM27358.1.
AL109983
, AL050320, AL133331, AL445589 Genomic DNA. Translation: CAM28300.1.
BC005205 mRNA. Translation: AAH05205.1. Sequence problems.
BC020656 mRNA. Translation: AAH20656.1.
BC150644 mRNA. Translation: AAI50645.1.
CCDSiCCDS13115.2. [Q9NUV7-1]
RefSeqiNP_060797.2. NM_018327.2. [Q9NUV7-1]
UniGeneiHs.425023.

3D structure databases

ProteinModelPortaliQ9NUV7.
SMRiQ9NUV7. Positions 162-527.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-60753N.
STRINGi9606.ENSP00000381968.

Chemistry

GuidetoPHARMACOLOGYi2511.

PTM databases

PhosphoSiteiQ9NUV7.

Polymorphism and mutation databases

BioMutaiSPTLC3.
DMDMi158931158.

Proteomic databases

MaxQBiQ9NUV7.
PaxDbiQ9NUV7.
PRIDEiQ9NUV7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000399002; ENSP00000381968; ENSG00000172296.
GeneIDi55304.
KEGGihsa:55304.
UCSCiuc002woc.3. human. [Q9NUV7-2]
uc002wod.1. human. [Q9NUV7-1]

Organism-specific databases

CTDi55304.
GeneCardsiGC20P012938.
H-InvDBHIX0019548.
HGNCiHGNC:16253. SPTLC3.
HPAiHPA044247.
MIMi611120. gene.
neXtProtiNX_Q9NUV7.
PharmGKBiPA162404677.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0156.
GeneTreeiENSGT00550000074678.
HOVERGENiHBG002230.
InParanoidiQ9NUV7.
KOiK00654.
OMAiNGNLHNH.
OrthoDBiEOG73RBB0.
PhylomeDBiQ9NUV7.
TreeFamiTF300452.

Enzyme and pathway databases

UniPathwayiUPA00222.
BioCyciMetaCyc:HS16070-MONOMER.
BRENDAi2.3.1.50. 2681.
ReactomeiREACT_115810. Sphingolipid de novo biosynthesis.

Miscellaneous databases

ChiTaRSiSPTLC3. human.
GenomeRNAii55304.
NextBioi59534.
PROiQ9NUV7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NUV7.
CleanExiHS_SPTLC3.
ExpressionAtlasiQ9NUV7. baseline and differential.
GenevisibleiQ9NUV7. HS.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase."
    Hornemann T., Richard S., Ruetti M.F., Wei Y., von Eckardstein A.
    J. Biol. Chem. 281:37275-37281(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), CATALYTIC ACTIVITY, TISSUE SPECIFICITY.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    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.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Placenta.
  3. "The DNA sequence and comparative analysis of human chromosome 20."
    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.
    Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT VAL-140.
    Tissue: Brain, Placenta and Urinary bladder.
  5. "Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities."
    Han G., Gupta S.D., Gable K., Niranjanakumari S., Moitra P., Eichler F., Brown R.H. Jr., Harmon J.M., Dunn T.M.
    Proc. Natl. Acad. Sci. U.S.A. 106:8186-8191(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION IN THE SPT COMPLEX.

Entry informationi

Entry nameiSPTC3_HUMAN
AccessioniPrimary (citable) accession number: Q9NUV7
Secondary accession number(s): A2A2I4
, B9EK64, Q05DQ8, Q5T1U4, Q9H1L1, Q9H1Z0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: October 2, 2007
Last modified: July 22, 2015
This is version 119 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.