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O60906

- NSMA_HUMAN

UniProt

O60906 - NSMA_HUMAN

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Protein

Sphingomyelin phosphodiesterase 2

Gene

SMPD2

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

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

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
Complete GO annotation...

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

Topology

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

GO - Cellular componenti

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

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. 8 interactions.
STRINGi9606.ENSP00000258052.

Structurei

3D structure databases

ProteinModelPortaliO60906.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the neutral sphingomyelinase family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG269293.
GeneTreeiENSGT00390000009166.
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

        10         20         30         40         50
MKPNFSLRLR IFNLNCWGIP YLSKHRADRM RRLGDFLNQE SFDLALLEEV
60 70 80 90 100
WSEQDFQYLR QKLSPTYPAA HHFRSGIIGS GLCVFSKHPI QELTQHIYTL
110 120 130 140 150
NGYPYMIHHG DWFSGKAVGL LVLHLSGMVL NAYVTHLHAE YNRQKDIYLA
160 170 180 190 200
HRVAQAWELA QFIHHTSKKA DVVLLCGDLN MHPEDLGCCL LKEWTGLHDA
210 220 230 240 250
YLETRDFKGS EEGNTMVPKN CYVSQQELKP FPFGVRIDYV LYKAVSGFYI
260 270 280 290 300
SCKSFETTTG FDPHRGTPLS DHEALMATLF VRHSPPQQNP SSTHGPAERS
310 320 330 340 350
PLMCVLKEAW TELGLGMAQA RWWATFASYV IGLGLLLLAL LCVLAAGGGA
360 370 380 390 400
GEAAILLWTP SVGLVLWAGA FYLFHVQEVN GLYRAQAELQ HVLGRAREAQ
410 420
DLGPEPQPAL LLGQQEGDRT KEQ
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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. 8 interactions.
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.
GeneTreei ENSGT00390000009166.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 129 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