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O60906 (NSMA_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 123. 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·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:SMPD2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length423 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

Sphingomyelin + H2O = N-acylsphingosine + phosphocholine.

Cofactor

Magnesium.

Pathway

Lipid metabolism; sphingolipid metabolism.

Subcellular location

Membrane; Multi-pass membrane protein.

Sequence similarities

Belongs to the neutral sphingomyelinase family.

Biophysicochemical properties

pH dependence:

Optimum pH is 6.5-7.5.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 423423Sphingomyelin phosphodiesterase 2
PRO_0000075686

Regions

Transmembrane330 – 35021Helical; Potential
Transmembrane354 – 37421Helical; Potential

Sites

Active site2721Proton acceptor By similarity
Metal binding491Magnesium By similarity
Site1801Important for substrate recognition By similarity

Natural variations

Natural variant31P → L. Ref.1
Corresponds to variant rs1048197 [ dbSNP | Ensembl ].
VAR_050305
Natural variant2231V → I.
Corresponds to variant rs9386806 [ dbSNP | Ensembl ].
VAR_050306
Natural variant2651R → S. Ref.1 Ref.3
Corresponds to variant rs1476387 [ dbSNP | Ensembl ].
VAR_024181

Sequences

Sequence LengthMass (Da)Tools
O60906 [UniParc].

Last modified November 13, 2007. Version 2.
Checksum: 3C1514CE21560501

FASTA42347,646
        10         20         30         40         50         60 
MKPNFSLRLR IFNLNCWGIP YLSKHRADRM RRLGDFLNQE SFDLALLEEV WSEQDFQYLR 

        70         80         90        100        110        120 
QKLSPTYPAA HHFRSGIIGS GLCVFSKHPI QELTQHIYTL NGYPYMIHHG DWFSGKAVGL 

       130        140        150        160        170        180 
LVLHLSGMVL NAYVTHLHAE YNRQKDIYLA HRVAQAWELA QFIHHTSKKA DVVLLCGDLN 

       190        200        210        220        230        240 
MHPEDLGCCL LKEWTGLHDA YLETRDFKGS EEGNTMVPKN CYVSQQELKP FPFGVRIDYV 

       250        260        270        280        290        300 
LYKAVSGFYI SCKSFETTTG FDPHRGTPLS DHEALMATLF VRHSPPQQNP SSTHGPAERS 

       310        320        330        340        350        360 
PLMCVLKEAW TELGLGMAQA RWWATFASYV IGLGLLLLAL LCVLAAGGGA GEAAILLWTP 

       370        380        390        400        410        420 
SVGLVLWAGA FYLFHVQEVN GLYRAQAELQ HVLGRAREAQ DLGPEPQPAL LLGQQEGDRT 


KEQ 

« Hide

References

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

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ222801 mRNA. Translation: CAA10995.1.
AL109947 Genomic DNA. Translation: CAI23338.1.
BC000038 mRNA. Translation: AAH00038.1.
RefSeqNP_003071.2. NM_003080.2.
UniGeneHs.55235.

3D structure databases

ProteinModelPortalO60906.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112494. 1 interaction.
STRING9606.ENSP00000258052.

Chemistry

BindingDBO60906.
ChEMBLCHEMBL4712.

PTM databases

PhosphoSiteO60906.

Proteomic databases

PaxDbO60906.
PRIDEO60906.

Protocols and materials databases

DNASU6610.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000258052; ENSP00000258052; ENSG00000135587.
GeneID6610.
KEGGhsa:6610.
UCSCuc003pti.3. human.

Organism-specific databases

CTD6610.
GeneCardsGC06P109761.
H-InvDBHIX0006125.
HGNCHGNC:11121. SMPD2.
HPAHPA018110.
HPA018125.
MIM603498. gene.
neXtProtNX_O60906.
PharmGKBPA35970.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG269293.
HOGENOMHOG000044683.
HOVERGENHBG019089.
InParanoidO60906.
KOK12351.
OMAQARWWAT.
OrthoDBEOG7SXW3M.
PhylomeDBO60906.
TreeFamTF313899.

Enzyme and pathway databases

BRENDA3.1.4.12. 2681.
ReactomeREACT_111102. Signal Transduction.
REACT_111217. Metabolism.
UniPathwayUPA00222.

Gene expression databases

BgeeO60906.
CleanExHS_SMPD2.
GenevestigatorO60906.

Family and domain databases

Gene3D3.60.10.10. 1 hit.
InterProIPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PfamPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
SUPFAMSSF56219. SSF56219. 1 hit.
ProtoNetSearch...

Other

GeneWikiSMPD2.
GenomeRNAi6610.
NextBio25735.
PROO60906.
SOURCESearch...

Entry information

Entry nameNSMA_HUMAN
AccessionPrimary (citable) accession number: O60906
Secondary accession number(s): Q5TED1, Q9BWR3
Entry history
Integrated into UniProtKB/Swiss-Prot: February 11, 2002
Last sequence update: November 13, 2007
Last modified: April 16, 2014
This is version 123 of the entry and version 2 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 6

Human chromosome 6: entries, gene names and cross-references to MIM