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Q9NUV7 (SPTC3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 110. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:SPTLC3
Synonyms:C20orf38, SPTLC2L
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length552 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.5

Catalytic activity

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2. Ref.1 Ref.5

Cofactor

Pyridoxal phosphate By similarity.

Pathway

Lipid metabolism; sphingolipid metabolism.

Subunit structure

Heterodimer with SPTLC1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1/SPTLC1, LCB2 (SPTLC2 or SPTLC3) and ssPT (SPTSSA and SPTSSB). Ref.5

Subcellular location

Endoplasmic reticulum membrane; Single-pass membrane protein By similarity.

Tissue specificity

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

Sequence similarities

Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.

Sequence caution

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

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9NUV7-1)

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.
Isoform 2 (identifier: Q9NUV7-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 552552Serine palmitoyltransferase 3
PRO_0000079426

Regions

Transmembrane59 – 7921Helical; Potential

Amino acid modifications

Modified residue3711N6-(pyridoxal phosphate)lysine By similarity

Natural variations

Alternative sequence102 – 17574DFVPL…LGLAA → VRMRTSLDLCQCLLLSKVFS EVVMQVQILESMRCSGTIQG KFHSSPPPKPHYPWAYGPVF TNISWATTICHIPN in isoform 2.
VSP_028167
Alternative sequence176 – 552377Missing in isoform 2.
VSP_028168
Natural variant1401L → V. Ref.4
Corresponds to variant rs243887 [ dbSNP | Ensembl ].
VAR_048230
Isoform 2:
Natural variant1491P → A.
Corresponds to variant rs934335 [ dbSNP | Ensembl ].

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 2, 2007. Version 3.
Checksum: EED341220DCA683A

FASTA55262,049
        10         20         30         40         50         60 
MANPGGGAVC NGKLHNHKKQ SNGSQSRNCT KNGIVKEAQQ NGKPHFYDKL IVESFEEAPL 

        70         80         90        100        110        120 
HVMVFTYMGY GIGTLFGYLR DFLRNWGIEK CNAAVERKEQ KDFVPLYQDF ENFYTRNLYM 

       130        140        150        160        170        180 
RIRDNWNRPI CSAPGPLFDL MERVSDDYNW TFRFTGRVIK DVINMGSYNF LGLAAKYDES 

       190        200        210        220        230        240 
MRTIKDVLEV YGTGVASTRH EMGTLDKHKE LEDLVAKFLN VEAAMVFGMG FATNSMNIPA 

       250        260        270        280        290        300 
LVGKGCLILS DELNHTSLVL GARLSGATIR IFKHNNTQSL EKLLRDAVIY GQPRTRRAWK 

       310        320        330        340        350        360 
KILILVEGVY SMEGSIVHLP QIIALKKKYK AYLYIDEAHS IGAVGPTGRG VTEFFGLDPH 

       370        380        390        400        410        420 
EVDVLMGTFT KSFGASGGYI AGRKDLVDYL RVHSHSAVYA SSMSPPIAEQ IIRSLKLIMG 

       430        440        450        460        470        480 
LDGTTQGLQR VQQLAKNTRY FRQRLQEMGF IIYGNENASV VPLLLYMPGK VAAFARHMLE 

       490        500        510        520        530        540 
KKIGVVVVGF PATPLAEARA RFCVSAAHTR EMLDTVLEAL DEMGDLLQLK YSRHKKSARP 

       550 
ELYDETSFEL ED 

« Hide

Isoform 2 [UniParc].

Checksum: 0B52D6020D5F73F3
Show »

FASTA17519,693

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK001974 mRNA. Translation: BAA92012.1.
AL133331 expand/collapse EMBL AC list , AL050320, AL109983, AL445589 Genomic DNA. Translation: CAM13116.1.
AL445589 expand/collapse EMBL AC list , AL050320, AL109983, AL133331 Genomic DNA. Translation: CAM16427.1.
AL050320 expand/collapse EMBL AC list , AL109983, AL133331, AL445589 Genomic DNA. Translation: CAM27358.1.
AL109983 expand/collapse EMBL AC list , 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.
CCDSCCDS13115.2. [Q9NUV7-1]
RefSeqNP_060797.2. NM_018327.2. [Q9NUV7-1]
UniGeneHs.425023.

3D structure databases

ProteinModelPortalQ9NUV7.
SMRQ9NUV7. Positions 109-529.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-60753N.
STRING9606.ENSP00000381968.

Chemistry

DrugBankDB00114. Pyridoxal Phosphate.
GuidetoPHARMACOLOGY2511.

PTM databases

PhosphoSiteQ9NUV7.

Polymorphism databases

DMDM158931158.

Proteomic databases

MaxQBQ9NUV7.
PaxDbQ9NUV7.
PRIDEQ9NUV7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000399002; ENSP00000381968; ENSG00000172296. [Q9NUV7-1]
GeneID55304.
KEGGhsa:55304.
UCSCuc002woc.3. human. [Q9NUV7-2]
uc002wod.1. human. [Q9NUV7-1]

Organism-specific databases

CTD55304.
GeneCardsGC20P012938.
H-InvDBHIX0019548.
HGNCHGNC:16253. SPTLC3.
HPAHPA044247.
MIM611120. gene.
neXtProtNX_Q9NUV7.
PharmGKBPA162404677.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0156.
HOVERGENHBG002230.
InParanoidQ9NUV7.
KOK00654.
OMASLKLIMG.
OrthoDBEOG73RBB0.
PhylomeDBQ9NUV7.
TreeFamTF300452.

Enzyme and pathway databases

BioCycMetaCyc:HS16070-MONOMER.
ReactomeREACT_111217. Metabolism.
UniPathwayUPA00222.

Gene expression databases

ArrayExpressQ9NUV7.
BgeeQ9NUV7.
CleanExHS_SPTLC3.
GenevestigatorQ9NUV7.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProIPR001917. 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]
PfamPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMSSF53383. SSF53383. 1 hit.
PROSITEPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSPTLC3. human.
GenomeRNAi55304.
NextBio59534.
PROQ9NUV7.
SOURCESearch...

Entry information

Entry nameSPTC3_HUMAN
AccessionPrimary (citable) accession number: Q9NUV7
Secondary accession number(s): A2A2I4 expand/collapse secondary AC list , B9EK64, Q05DQ8, Q5T1U4, Q9H1L1, Q9H1Z0
Entry history
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: October 2, 2007
Last modified: July 9, 2014
This is version 110 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM