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Protein

Sphingomyelin phosphodiesterase 2

Gene

SMPD2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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: sphingolipid metabolism

This protein is involved in the pathway sphingolipid metabolism, which is part of Lipid metabolism.
View all proteins of this organism that are known to be involved in the pathway sphingolipid metabolism and in Lipid metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi49MagnesiumBy similarity1
Sitei180Important for substrate recognitionBy similarity1
Active sitei272Proton acceptorBy similarity1

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • sphingomyelin phosphodiesterase activity Source: ProtInc

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processLipid metabolism, Sphingolipid metabolism
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.4.12 2681
ReactomeiR-HSA-1660662 Glycosphingolipid metabolism
R-HSA-193681 Ceramide signalling
R-HSA-5626978 TNFR1-mediated ceramide production
UniPathwayi
UPA00222

Chemistry databases

SwissLipidsiSLP:000000174

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
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000135587.8
HGNCiHGNC:11121 SMPD2
MIMi603498 gene
neXtProtiNX_O60906

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei330 – 350HelicalSequence analysisAdd BLAST21
Transmembranei354 – 374HelicalSequence analysisAdd BLAST21

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi6610
OpenTargetsiENSG00000135587
PharmGKBiPA35970

Chemistry databases

ChEMBLiCHEMBL4712

Polymorphism and mutation databases

BioMutaiSMPD2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000756861 – 423Sphingomyelin phosphodiesterase 2Add BLAST423

Proteomic databases

EPDiO60906
MaxQBiO60906
PaxDbiO60906
PeptideAtlasiO60906
PRIDEiO60906
ProteomicsDBi49663

PTM databases

iPTMnetiO60906
PhosphoSitePlusiO60906

Expressioni

Gene expression databases

BgeeiENSG00000135587 Expressed in 151 organ(s), highest expression level in left testis
CleanExiHS_SMPD2
ExpressionAtlasiO60906 baseline and differential
GenevisibleiO60906 HS

Organism-specific databases

HPAiHPA018110
HPA018125

Interactioni

Protein-protein interaction databases

BioGridi112494, 30 interactors
IntActiO60906, 13 interactors
STRINGi9606.ENSP00000258052

Chemistry databases

BindingDBiO60906

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

eggNOGiKOG3873 Eukaryota
ENOG410ZFPY LUCA
GeneTreeiENSGT00390000009166
HOGENOMiHOG000044683
HOVERGENiHBG019089
InParanoidiO60906
KOiK12351
OMAiRIQHADW
OrthoDBiEOG091G0EZ8
PhylomeDBiO60906
TreeFamiTF313899

Family and domain databases

Gene3Di3.60.10.10, 1 hit
InterProiView protein in InterPro
IPR036691 Endo/exonu/phosph_ase_sf
IPR005135 Endo/exonuclease/phosphatase
IPR038772 SMPD2-like
PANTHERiPTHR12393 PTHR12393, 1 hit
PfamiView protein in Pfam
PF03372 Exo_endo_phos, 1 hit
SUPFAMiSSF56219 SSF56219, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y5N2H0Y5N2_HUMAN
Sphingomyelin phosphodiesterase 2
SMPD2
204Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0503053P → L1 PublicationCorresponds to variant dbSNP:rs1048197Ensembl.1
Natural variantiVAR_050306223V → I. Corresponds to variant dbSNP:rs9386806Ensembl.1
Natural variantiVAR_024181265R → S2 PublicationsCorresponds to variant dbSNP:rs1476387Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ222801 mRNA Translation: CAA10995.1
AL109947 Genomic DNA No translation available.
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.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ222801 mRNA Translation: CAA10995.1
AL109947 Genomic DNA No translation available.
BC000038 mRNA Translation: AAH00038.1
CCDSiCCDS5075.1
RefSeqiNP_003071.2, NM_003080.2
UniGeneiHs.55235

3D structure databases

ProteinModelPortaliO60906
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112494, 30 interactors
IntActiO60906, 13 interactors
STRINGi9606.ENSP00000258052

Chemistry databases

BindingDBiO60906
ChEMBLiCHEMBL4712
SwissLipidsiSLP:000000174

PTM databases

iPTMnetiO60906
PhosphoSitePlusiO60906

Polymorphism and mutation databases

BioMutaiSMPD2

Proteomic databases

EPDiO60906
MaxQBiO60906
PaxDbiO60906
PeptideAtlasiO60906
PRIDEiO60906
ProteomicsDBi49663

Protocols and materials databases

DNASUi6610
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000258052; ENSP00000258052; ENSG00000135587
GeneIDi6610
KEGGihsa:6610
UCSCiuc003pti.4 human

Organism-specific databases

CTDi6610
DisGeNETi6610
EuPathDBiHostDB:ENSG00000135587.8
GeneCardsiSMPD2
H-InvDBiHIX0006125
HGNCiHGNC:11121 SMPD2
HPAiHPA018110
HPA018125
MIMi603498 gene
neXtProtiNX_O60906
OpenTargetsiENSG00000135587
PharmGKBiPA35970
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3873 Eukaryota
ENOG410ZFPY LUCA
GeneTreeiENSGT00390000009166
HOGENOMiHOG000044683
HOVERGENiHBG019089
InParanoidiO60906
KOiK12351
OMAiRIQHADW
OrthoDBiEOG091G0EZ8
PhylomeDBiO60906
TreeFamiTF313899

Enzyme and pathway databases

UniPathwayi
UPA00222

BRENDAi3.1.4.12 2681
ReactomeiR-HSA-1660662 Glycosphingolipid metabolism
R-HSA-193681 Ceramide signalling
R-HSA-5626978 TNFR1-mediated ceramide production

Miscellaneous databases

GeneWikiiSMPD2
GenomeRNAii6610
PROiPR:O60906
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000135587 Expressed in 151 organ(s), highest expression level in left testis
CleanExiHS_SMPD2
ExpressionAtlasiO60906 baseline and differential
GenevisibleiO60906 HS

Family and domain databases

Gene3Di3.60.10.10, 1 hit
InterProiView protein in InterPro
IPR036691 Endo/exonu/phosph_ase_sf
IPR005135 Endo/exonuclease/phosphatase
IPR038772 SMPD2-like
PANTHERiPTHR12393 PTHR12393, 1 hit
PfamiView protein in Pfam
PF03372 Exo_endo_phos, 1 hit
SUPFAMiSSF56219 SSF56219, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiNSMA_HUMAN
AccessioniPrimary (citable) accession number: O60906
Secondary accession number(s): Q5TED1, Q9BWR3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 11, 2002
Last sequence update: November 13, 2007
Last modified: September 12, 2018
This is version 157 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  4. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  5. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  6. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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