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Protein

Acid sphingomyelinase-like phosphodiesterase 3b

Gene

SMPDL3B

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

Functioni

Lipid-modulating phosphodiesterase (PubMed:26095358). Active on the surface of macrophages and dendritic cells and strongly influences macrophage lipid composition and membrane fluidity. Acts as a negative regulator of Toll-like receptor signaling (By similarity).By similarity1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi28 – 281Zinc 1By similarity
Metal bindingi30 – 301Zinc 1By similarity
Metal bindingi93 – 931Zinc 1By similarity
Metal bindingi93 – 931Zinc 2By similarity
Metal bindingi134 – 1341Zinc 2By similarity
Metal bindingi236 – 2361Zinc 2By similarity
Metal bindingi277 – 2771Zinc 2By similarity
Metal bindingi279 – 2791Zinc 1By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Immunity, Inflammatory response, Innate immunity, Lipid degradation, Lipid metabolism

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Acid sphingomyelinase-like phosphodiesterase 3b (EC:3.1.4.-1 Publication)
Short name:
ASM-like phosphodiesterase 3b
Gene namesi
Name:SMPDL3B
Synonyms:ASML3B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:21416. SMPDL3B.

Subcellular locationi

  • Secreted By similarity
  • Cell membrane By similarity; Lipid-anchorGPI-anchor By similarity

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • extracellular space Source: UniProtKB
  • plasma membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane, Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi135 – 1351H → A: Reduced phosphodiesterase activity. 1 Publication

Organism-specific databases

PharmGKBiPA134889099.

Polymorphism and mutation databases

BioMutaiSMPDL3B.
DMDMi62906890.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Sequence analysisAdd
BLAST
Chaini19 – 455437Acid sphingomyelinase-like phosphodiesterase 3bPRO_0000002331Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi45 ↔ 64By similarity
Glycosylationi72 – 721N-linked (GlcNAc...)Sequence analysis
Glycosylationi164 – 1641N-linked (GlcNAc...)Sequence analysis
Glycosylationi343 – 3431N-linked (GlcNAc...)Sequence analysis
Disulfide bondi415 ↔ 428By similarity

Post-translational modificationi

N-glycosylated.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein, GPI-anchor, Lipoprotein

Proteomic databases

EPDiQ92485.
MaxQBiQ92485.
PaxDbiQ92485.
PRIDEiQ92485.

PTM databases

iPTMnetiQ92485.
PhosphoSiteiQ92485.

Expressioni

Gene expression databases

BgeeiQ92485.
CleanExiHS_SMPDL3B.
ExpressionAtlasiQ92485. baseline and differential.
GenevisibleiQ92485. HS.

Organism-specific databases

HPAiHPA030561.

Interactioni

Subunit structurei

Interacts with TLR4, TLR7, TLR8 and TLR9.By similarity

Protein-protein interaction databases

BioGridi118117. 8 interactions.
MINTiMINT-5006501.
STRINGi9606.ENSP00000363001.

Structurei

3D structure databases

ProteinModelPortaliQ92485.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the acid sphingomyelinase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410ISVB. Eukaryota.
ENOG410XRWF. LUCA.
GeneTreeiENSGT00530000063095.
HOGENOMiHOG000294197.
HOVERGENiHBG050594.
InParanoidiQ92485.
KOiK01128.
OMAiKCPNRIS.
OrthoDBiEOG7XPZ70.
PhylomeDBiQ92485.
TreeFamiTF313674.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
InterProiIPR017064. ASM-like_Pdiesterase_prd.
IPR004843. Calcineurin-like_PHP_apaH.
IPR029052. Metallo-depent_PP-like.
[Graphical view]
PfamiPF00149. Metallophos. 1 hit.
[Graphical view]
PIRSFiPIRSF036767. ASM-like_PDE. 1 hit.
SUPFAMiSSF56300. SSF56300. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q92485-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MRLLAWLIFL ANWGGARAEP GKFWHIADLH LDPDYKVSKD PFQVCPSAGS
60 70 80 90 100
QPVPDAGPWG DYLCDSPWAL INSSIYAMKE IEPEPDFILW TGDDTPHVPD
110 120 130 140 150
EKLGEAAVLE IVERLTKLIR EVFPDTKVYA ALGNHDFHPK NQFPAGSNNI
160 170 180 190 200
YNQIAELWKP WLSNESIALF KKGAFYCEKL PGPSGAGRIV VLNTNLYYTS
210 220 230 240 250
NALTADMADP GQQFQWLEDV LTDASKAGDM VYIVGHVPPG FFEKTQNKAW
260 270 280 290 300
FREGFNEKYL KVVRKHHRVI AGQFFGHHHT DSFRMLYDDA GVPISAMFIT
310 320 330 340 350
PGVTPWKTTL PGVVNGANNP AIRVFEYDRA TLSLKDMVTY FMNLSQANAQ
360 370 380 390 400
GTPRWELEYQ LTEAYGVPDA SAHSMHTVLD RIAGDQSTLQ RYYVYNSVSY
410 420 430 440 450
SAGVCDEACS MQHVCAMRQV DIDAYTTCLY ASGTTPVPQL PLLLMALLGL

CTLVL
Length:455
Mass (Da):50,814
Last modified:April 26, 2005 - v2
Checksum:iE947E49C3A8449BA
GO
Isoform 2 (identifier: Q92485-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     336-373: DMVTYFMNLS...AYGVPDASAH → VRSPAEARGG...LPLTTEPQEG
     374-455: Missing.

Note: No experimental confirmation available.
Show »
Length:373
Mass (Da):41,689
Checksum:i464DE3C94BCC1B49
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti375 – 3762MH → ID in CAA69328 (Ref. 1) Curated
Sequence conflicti453 – 4553LVL → TRAVTCQAHHSSW in CAA69328 (Ref. 1) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti381 – 3811R → H.
Corresponds to variant rs34560878 [ dbSNP | Ensembl ].
VAR_048340

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei336 – 37338DMVTY…DASAH → VRSPAEARGGGWEGLKCITT FPHSQLIHLPLTTEPQEG in isoform 2. 1 PublicationVSP_013478Add
BLAST
Alternative sequencei374 – 45582Missing in isoform 2. 1 PublicationVSP_013479Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08134 mRNA. Translation: CAA69328.1.
AK316500 mRNA. Translation: BAH14871.1.
AL512288 Genomic DNA. Translation: CAI14293.1.
AL512288 Genomic DNA. Translation: CAI14294.1.
CH471059 Genomic DNA. Translation: EAX07721.1.
BC014444 mRNA. Translation: AAH14444.1.
CCDSiCCDS30655.1. [Q92485-1]
CCDS30656.1. [Q92485-2]
RefSeqiNP_001009568.1. NM_001009568.2. [Q92485-2]
NP_055289.2. NM_014474.3. [Q92485-1]
UniGeneiHs.123659.

Genome annotation databases

EnsembliENST00000373888; ENSP00000362995; ENSG00000130768. [Q92485-2]
ENST00000373894; ENSP00000363001; ENSG00000130768. [Q92485-1]
GeneIDi27293.
KEGGihsa:27293.
UCSCiuc001bpf.4. human. [Q92485-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08134 mRNA. Translation: CAA69328.1.
AK316500 mRNA. Translation: BAH14871.1.
AL512288 Genomic DNA. Translation: CAI14293.1.
AL512288 Genomic DNA. Translation: CAI14294.1.
CH471059 Genomic DNA. Translation: EAX07721.1.
BC014444 mRNA. Translation: AAH14444.1.
CCDSiCCDS30655.1. [Q92485-1]
CCDS30656.1. [Q92485-2]
RefSeqiNP_001009568.1. NM_001009568.2. [Q92485-2]
NP_055289.2. NM_014474.3. [Q92485-1]
UniGeneiHs.123659.

3D structure databases

ProteinModelPortaliQ92485.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118117. 8 interactions.
MINTiMINT-5006501.
STRINGi9606.ENSP00000363001.

PTM databases

iPTMnetiQ92485.
PhosphoSiteiQ92485.

Polymorphism and mutation databases

BioMutaiSMPDL3B.
DMDMi62906890.

Proteomic databases

EPDiQ92485.
MaxQBiQ92485.
PaxDbiQ92485.
PRIDEiQ92485.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000373888; ENSP00000362995; ENSG00000130768. [Q92485-2]
ENST00000373894; ENSP00000363001; ENSG00000130768. [Q92485-1]
GeneIDi27293.
KEGGihsa:27293.
UCSCiuc001bpf.4. human. [Q92485-1]

Organism-specific databases

CTDi27293.
GeneCardsiSMPDL3B.
HGNCiHGNC:21416. SMPDL3B.
HPAiHPA030561.
neXtProtiNX_Q92485.
PharmGKBiPA134889099.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410ISVB. Eukaryota.
ENOG410XRWF. LUCA.
GeneTreeiENSGT00530000063095.
HOGENOMiHOG000294197.
HOVERGENiHBG050594.
InParanoidiQ92485.
KOiK01128.
OMAiKCPNRIS.
OrthoDBiEOG7XPZ70.
PhylomeDBiQ92485.
TreeFamiTF313674.

Miscellaneous databases

ChiTaRSiSMPDL3B. human.
GenomeRNAii27293.
NextBioi50252.
PROiQ92485.

Gene expression databases

BgeeiQ92485.
CleanExiHS_SMPDL3B.
ExpressionAtlasiQ92485. baseline and differential.
GenevisibleiQ92485. HS.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
InterProiIPR017064. ASM-like_Pdiesterase_prd.
IPR004843. Calcineurin-like_PHP_apaH.
IPR029052. Metallo-depent_PP-like.
[Graphical view]
PfamiPF00149. Metallophos. 1 hit.
[Graphical view]
PIRSFiPIRSF036767. ASM-like_PDE. 1 hit.
SUPFAMiSSF56300. SSF56300. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Acid sphingomyelinase is a member of a multi-gene family and shares motifs with a large family of metallo-phosphoesterases."
    Hofmann K.
    Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  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.
    , 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 1).
    Tissue: Trachea.
  3. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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] (ISOFORM 2).
    Tissue: Colon.
  6. Cited for: PHOSPHODIESTERASE ACTIVITY, MUTAGENESIS OF HIS-135, GLYCOSYLATION, CATALYTIC ACTIVITY.

Entry informationi

Entry nameiASM3B_HUMAN
AccessioniPrimary (citable) accession number: Q92485
Secondary accession number(s): B7ZB35, Q5T0Z0, Q96CB7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 29, 2001
Last sequence update: April 26, 2005
Last modified: May 11, 2016
This is version 124 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 1
    Human chromosome 1: 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. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.