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Q9NUV7

- SPTC3_HUMAN

UniProt

Q9NUV7 - SPTC3_HUMAN

Protein

Serine palmitoyltransferase 3

Gene

SPTLC3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 112 (01 Oct 2014)
      Sequence version 3 (02 Oct 2007)
      Previous versions | rss
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    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

    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

    GO - Cellular componenti

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

    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)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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

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

    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. 2 PublicationsVSP_028167Add
    BLAST
    Alternative sequencei176 – 552377Missing in isoform 2. 2 PublicationsVSP_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

    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

    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: October 1, 2014
    This is version 112 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