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O60906

- NSMA_HUMAN

UniProt

O60906 - NSMA_HUMAN

Protein

Sphingomyelin phosphodiesterase 2

Gene

SMPD2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 127 (01 Oct 2014)
      Sequence version 2 (13 Nov 2007)
      Previous versions | rss
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    Functioni

    Converts sphingomyelin to ceramide. Hydrolyze 1-acyl-2-lyso-sn-glycero-3-phosphocholine (lyso-PC) and 1-O-alkyl-2-lyso-sn-glycero-3-phosphocholine (lyso-platelet-activating factor). The physiological substrate seems to be Lyso-PAF.

    Catalytic activityi

    Sphingomyelin + H2O = N-acylsphingosine + phosphocholine.

    Cofactori

    Magnesium.

    pH dependencei

    Optimum pH is 6.5-7.5.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi49 – 491MagnesiumBy similarity
    Sitei180 – 1801Important for substrate recognitionBy similarity
    Active sitei272 – 2721Proton acceptorBy similarity

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. sphingomyelin phosphodiesterase activity Source: ProtInc

    GO - Biological processi

    1. apoptotic signaling pathway Source: Reactome
    2. ceramide biosynthetic process Source: Ensembl
    3. glycosphingolipid metabolic process Source: Reactome
    4. neurotrophin TRK receptor signaling pathway Source: Reactome
    5. response to mechanical stimulus Source: Ensembl
    6. small molecule metabolic process Source: Reactome
    7. sphingolipid metabolic process Source: Reactome
    8. sphingomyelin metabolic process Source: ProtInc

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Lipid metabolism, Sphingolipid metabolism

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BRENDAi3.1.4.12. 2681.
    ReactomeiREACT_116105. Glycosphingolipid metabolism.
    REACT_13806. Ceramide signalling.
    UniPathwayiUPA00222.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sphingomyelin phosphodiesterase 2 (EC:3.1.4.12)
    Alternative name(s):
    Lyso-platelet-activating factor-phospholipase C
    Short name:
    Lyso-PAF-PLC
    Neutral sphingomyelinase
    Short name:
    N-SMase
    Short name:
    nSMase
    Gene namesi
    Name:SMPD2
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 6

    Organism-specific databases

    HGNCiHGNC:11121. SMPD2.

    Subcellular locationi

    GO - Cellular componenti

    1. caveola Source: Ensembl
    2. integral component of plasma membrane Source: ProtInc
    3. plasma membrane Source: Reactome

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA35970.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 423423Sphingomyelin phosphodiesterase 2PRO_0000075686Add
    BLAST

    Proteomic databases

    MaxQBiO60906.
    PaxDbiO60906.
    PRIDEiO60906.

    PTM databases

    PhosphoSiteiO60906.

    Expressioni

    Gene expression databases

    BgeeiO60906.
    CleanExiHS_SMPD2.
    GenevestigatoriO60906.

    Organism-specific databases

    HPAiHPA018110.
    HPA018125.

    Interactioni

    Protein-protein interaction databases

    BioGridi112494. 1 interaction.
    STRINGi9606.ENSP00000258052.

    Structurei

    3D structure databases

    ProteinModelPortaliO60906.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei330 – 35021HelicalSequence AnalysisAdd
    BLAST
    Transmembranei354 – 37421HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the neutral sphingomyelinase family.Curated

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG269293.
    HOGENOMiHOG000044683.
    HOVERGENiHBG019089.
    InParanoidiO60906.
    KOiK12351.
    OMAiQARWWAT.
    OrthoDBiEOG7SXW3M.
    PhylomeDBiO60906.
    TreeFamiTF313899.

    Family and domain databases

    Gene3Di3.60.10.10. 1 hit.
    InterProiIPR005135. Endo/exonuclease/phosphatase.
    [Graphical view]
    PfamiPF03372. Exo_endo_phos. 1 hit.
    [Graphical view]
    SUPFAMiSSF56219. SSF56219. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O60906-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKPNFSLRLR IFNLNCWGIP YLSKHRADRM RRLGDFLNQE SFDLALLEEV    50
    WSEQDFQYLR QKLSPTYPAA HHFRSGIIGS GLCVFSKHPI QELTQHIYTL 100
    NGYPYMIHHG DWFSGKAVGL LVLHLSGMVL NAYVTHLHAE YNRQKDIYLA 150
    HRVAQAWELA QFIHHTSKKA DVVLLCGDLN MHPEDLGCCL LKEWTGLHDA 200
    YLETRDFKGS EEGNTMVPKN CYVSQQELKP FPFGVRIDYV LYKAVSGFYI 250
    SCKSFETTTG FDPHRGTPLS DHEALMATLF VRHSPPQQNP SSTHGPAERS 300
    PLMCVLKEAW TELGLGMAQA RWWATFASYV IGLGLLLLAL LCVLAAGGGA 350
    GEAAILLWTP SVGLVLWAGA FYLFHVQEVN GLYRAQAELQ HVLGRAREAQ 400
    DLGPEPQPAL LLGQQEGDRT KEQ 423
    Length:423
    Mass (Da):47,646
    Last modified:November 13, 2007 - v2
    Checksum:i3C1514CE21560501
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti3 – 31P → L.1 Publication
    Corresponds to variant rs1048197 [ dbSNP | Ensembl ].
    VAR_050305
    Natural varianti223 – 2231V → I.
    Corresponds to variant rs9386806 [ dbSNP | Ensembl ].
    VAR_050306
    Natural varianti265 – 2651R → S.2 Publications
    Corresponds to variant rs1476387 [ dbSNP | Ensembl ].
    VAR_024181

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ222801 mRNA. Translation: CAA10995.1.
    AL109947 Genomic DNA. Translation: CAI23338.1.
    BC000038 mRNA. Translation: AAH00038.1.
    CCDSiCCDS5075.1.
    RefSeqiNP_003071.2. NM_003080.2.
    UniGeneiHs.55235.

    Genome annotation databases

    EnsembliENST00000258052; ENSP00000258052; ENSG00000135587.
    GeneIDi6610.
    KEGGihsa:6610.
    UCSCiuc003pti.3. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ222801 mRNA. Translation: CAA10995.1 .
    AL109947 Genomic DNA. Translation: CAI23338.1 .
    BC000038 mRNA. Translation: AAH00038.1 .
    CCDSi CCDS5075.1.
    RefSeqi NP_003071.2. NM_003080.2.
    UniGenei Hs.55235.

    3D structure databases

    ProteinModelPortali O60906.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 112494. 1 interaction.
    STRINGi 9606.ENSP00000258052.

    Chemistry

    BindingDBi O60906.
    ChEMBLi CHEMBL4712.

    PTM databases

    PhosphoSitei O60906.

    Proteomic databases

    MaxQBi O60906.
    PaxDbi O60906.
    PRIDEi O60906.

    Protocols and materials databases

    DNASUi 6610.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000258052 ; ENSP00000258052 ; ENSG00000135587 .
    GeneIDi 6610.
    KEGGi hsa:6610.
    UCSCi uc003pti.3. human.

    Organism-specific databases

    CTDi 6610.
    GeneCardsi GC06P109761.
    H-InvDB HIX0006125.
    HGNCi HGNC:11121. SMPD2.
    HPAi HPA018110.
    HPA018125.
    MIMi 603498. gene.
    neXtProti NX_O60906.
    PharmGKBi PA35970.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG269293.
    HOGENOMi HOG000044683.
    HOVERGENi HBG019089.
    InParanoidi O60906.
    KOi K12351.
    OMAi QARWWAT.
    OrthoDBi EOG7SXW3M.
    PhylomeDBi O60906.
    TreeFami TF313899.

    Enzyme and pathway databases

    UniPathwayi UPA00222 .
    BRENDAi 3.1.4.12. 2681.
    Reactomei REACT_116105. Glycosphingolipid metabolism.
    REACT_13806. Ceramide signalling.

    Miscellaneous databases

    GeneWikii SMPD2.
    GenomeRNAii 6610.
    NextBioi 25735.
    PROi O60906.
    SOURCEi Search...

    Gene expression databases

    Bgeei O60906.
    CleanExi HS_SMPD2.
    Genevestigatori O60906.

    Family and domain databases

    Gene3Di 3.60.10.10. 1 hit.
    InterProi IPR005135. Endo/exonuclease/phosphatase.
    [Graphical view ]
    Pfami PF03372. Exo_endo_phos. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56219. SSF56219. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Cloned mammalian neutral sphingomyelinase: functions in sphingolipid signaling?"
      Tomiuk S., Hofmann K., Nix M., Zumbansen M., Stoffel W.
      Proc. Natl. Acad. Sci. U.S.A. 95:3638-3643(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], CHARACTERIZATION, TISSUE SPECIFICITY, VARIANTS LEU-3 AND SER-265.
    2. "The DNA sequence and analysis of human chromosome 6."
      Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
      , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
      Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "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], VARIANT SER-265.
      Tissue: Brain.
    4. "Function of the cloned putative neutral sphingomyelinase as lyso-platelet activating factor-phospholipase C."
      Sawai H., Domae N., Nagan N., Hannun Y.A.
      J. Biol. Chem. 274:38131-38139(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.

    Entry informationi

    Entry nameiNSMA_HUMAN
    AccessioniPrimary (citable) accession number: O60906
    Secondary accession number(s): Q5TED1, Q9BWR3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 11, 2002
    Last sequence update: November 13, 2007
    Last modified: October 1, 2014
    This is version 127 of the entry and version 2 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 6
      Human chromosome 6: 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