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Q9NUV7

- SPTC3_HUMAN

UniProt

Q9NUV7 - SPTC3_HUMAN

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Protein

Serine palmitoyltransferase 3

Gene
SPTLC3, C20orf38, SPTLC2L
Organism
Homo sapiens (Human)
Status
Reviewed - 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

Pyridoxal phosphate By similarity.

Pathwayi

GO - Molecular functioni

  1. pyridoxal phosphate binding Source: InterPro
  2. serine C-palmitoyltransferase activity Source: UniProtKB

GO - Biological processi

  1. small molecule metabolic process Source: Reactome
  2. sphingoid biosynthetic process Source: MGI
  3. sphingolipid biosynthetic process Source: UniProtKB
  4. 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.
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: Chromosome 20

Organism-specific databases

HGNCiHGNC:16253. SPTLC3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei59 – 7921Helical; Reviewed predictionAdd
BLAST

GO - Cellular componenti

  1. endoplasmic reticulum membrane Source: Reactome
  2. integral component of membrane Source: UniProtKB-KW
  3. serine C-palmitoyltransferase complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162404677.

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)lysine By 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

ArrayExpressiQ9NUV7.
BgeeiQ9NUV7.
CleanExiHS_SPTLC3.
GenevestigatoriQ9NUV7.

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 109-529.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
HOVERGENiHBG002230.
InParanoidiQ9NUV7.
KOiK00654.
OMAiSLKLIMG.
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. Align

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

MANPGGGAVC NGKLHNHKKQ SNGSQSRNCT KNGIVKEAQQ NGKPHFYDKL    50
IVESFEEAPL HVMVFTYMGY GIGTLFGYLR DFLRNWGIEK CNAAVERKEQ 100
KDFVPLYQDF ENFYTRNLYM RIRDNWNRPI CSAPGPLFDL MERVSDDYNW 150
TFRFTGRVIK DVINMGSYNF LGLAAKYDES MRTIKDVLEV YGTGVASTRH 200
EMGTLDKHKE LEDLVAKFLN VEAAMVFGMG FATNSMNIPA LVGKGCLILS 250
DELNHTSLVL GARLSGATIR IFKHNNTQSL EKLLRDAVIY GQPRTRRAWK 300
KILILVEGVY SMEGSIVHLP QIIALKKKYK AYLYIDEAHS IGAVGPTGRG 350
VTEFFGLDPH EVDVLMGTFT KSFGASGGYI AGRKDLVDYL RVHSHSAVYA 400
SSMSPPIAEQ IIRSLKLIMG LDGTTQGLQR VQQLAKNTRY FRQRLQEMGF 450
IIYGNENASV VPLLLYMPGK VAAFARHMLE KKIGVVVVGF PATPLAEARA 500
RFCVSAAHTR EMLDTVLEAL DEMGDLLQLK YSRHKKSARP ELYDETSFEL 550
ED 552
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. Reason: Contaminating sequence. Potential poly-A sequence.

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. VSP_028167Add
BLAST
Alternative sequencei176 – 552377Missing in isoform 2. VSP_028168Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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. [Q9NUV7-1]
GeneIDi55304.
KEGGihsa:55304.
UCSCiuc002woc.3. human. [Q9NUV7-2]
uc002wod.1. human. [Q9NUV7-1]

Polymorphism databases

DMDMi158931158.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS13115.2. [Q9NUV7-1 ]
RefSeqi NP_060797.2. NM_018327.2. [Q9NUV7-1 ]
UniGenei Hs.425023.

3D structure databases

ProteinModelPortali Q9NUV7.
SMRi Q9NUV7. Positions 109-529.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-60753N.
STRINGi 9606.ENSP00000381968.

Chemistry

DrugBanki DB00114. Pyridoxal Phosphate.
GuidetoPHARMACOLOGYi 2511.

PTM databases

PhosphoSitei Q9NUV7.

Polymorphism databases

DMDMi 158931158.

Proteomic databases

MaxQBi Q9NUV7.
PaxDbi Q9NUV7.
PRIDEi Q9NUV7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000399002 ; ENSP00000381968 ; ENSG00000172296 . [Q9NUV7-1 ]
GeneIDi 55304.
KEGGi hsa:55304.
UCSCi uc002woc.3. human. [Q9NUV7-2 ]
uc002wod.1. human. [Q9NUV7-1 ]

Organism-specific databases

CTDi 55304.
GeneCardsi GC20P012938.
H-InvDB HIX0019548.
HGNCi HGNC:16253. SPTLC3.
HPAi HPA044247.
MIMi 611120. gene.
neXtProti NX_Q9NUV7.
PharmGKBi PA162404677.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0156.
HOVERGENi HBG002230.
InParanoidi Q9NUV7.
KOi K00654.
OMAi SLKLIMG.
OrthoDBi EOG73RBB0.
PhylomeDBi Q9NUV7.
TreeFami TF300452.

Enzyme and pathway databases

UniPathwayi UPA00222 .
BioCyci MetaCyc:HS16070-MONOMER.
Reactomei REACT_115810. Sphingolipid de novo biosynthesis.

Miscellaneous databases

ChiTaRSi SPTLC3. human.
GenomeRNAii 55304.
NextBioi 59534.
PROi Q9NUV7.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q9NUV7.
Bgeei Q9NUV7.
CleanExi HS_SPTLC3.
Genevestigatori Q9NUV7.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProi IPR001917. 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 ]
Pfami PF00155. Aminotran_1_2. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 1 hit.
PROSITEi PS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 111 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

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