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Information on EC 3.1.4.41 - sphingomyelin phosphodiesterase D and Organism(s) Loxosceles laeta and UniProt Accession Q8I914
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3.1.4.41 sphingomyelin phosphodiesterase DIUBMB Comments
Does not act on phosphatidylcholine, but hydrolyses 2-lysophosphatidylcholine to choline and 2-lysophosphatidate.
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Word Map
- 3.1.4.41
- spider
- loxosceles
-
dermonecrosis
- smases
-
envenom
- laeta
- intermedia
-
bite
- reclusa
- damselae
- sphingomyelinases
-
photobacterium
- gaucho
- sicarius
- antivenoms
-
arachnid
-
phospholipase-d
- medicine
- biotechnology
The taxonomic range for the selected organisms is: Loxosceles laeta
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
smase d, sphingomyelinase d, glycerophosphoryl diester phosphodiesterase, smased, damselysin, lgrec1, sphingomyelinase-d, phospholipase d 1, sphingomyelin-specific phospholipase d, smase-d, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
damselysin
-
-
-
-
SMase D
SMD
sphingomyelinase D
SMD
-
-
-
-
sphingomyelinase D
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
sphingomyelin ceramide-phosphohydrolase
Does not act on phosphatidylcholine, but hydrolyses 2-lysophosphatidylcholine to choline and 2-lysophosphatidate.
CAS REGISTRY NUMBER
COMMENTARY
54992-31-3
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
sphingomyelin + H2O
choline + ceramide phosphate
Mg2+-ion-dependent acid-base mechanism which involves two histidines
-
-
?
1-O-hexadecylglycero-3-phosphocholine + H2O
choline + 1-O-hexadecylglycero-3-phosphate
-
i.e. lyso-platelet-activating factor
-
?
1-octanoyl-2-hydroxy-sn-glycero-3-phosphocholine + H2O
1-octanoyl-sn-glycero-2,3-cyclic-phosphate + choline
-
Loxosceles whole venoms cleanly convert 8:0 LPC substrate to 8:0 CPA product
-
-
?
1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine + H2O
1-palmitoyl-sn-glycero-2,3-cyclic-phosphate + choline
-
Loxosceles whole venoms and recombinant enzyme
-
-
?
N-lauroyl-D-erythro-sphingosylphosphorylcholine + H2O
lauroyl ceramide-1-phosphate + choline
-
-
-
-
?
lysophosphatidylcholine + H2O
lysophosphatidic acid + choline
-
-
-
?
sphingomyelin + H2O
ceramide 1-phosphate + choline
-
substrate as sphingomyelin/cholesterol multilamellar liposomes in a molar ratio of 2:1
-
-
?
sphingomyelin + H2O
ceramide phosphate + choline
-
-
-
-
?
additional information
?
-
-
no substrate: sphingosylphosphorylcholine
-
?
additional information
?
-
-
the recombinant protein rLIPLD1 shows hydrolytic activity on sphingomyelin and in vitro hemolytic activity on human red blood cells, whereas rLIPLD2 is inactive
-
-
?
additional information
?
-
-
the spider venom enzyme cleaves the substrates sphingomyelin and lysophosphatidylcholine in mammalian tissues, releasing the choline head group
-
-
?
additional information
?
-
-
recombinant enzymes, as well as whole venoms from diverse Loxosceles species, exclusively catalyze transphosphatidylation rather than hydrolysis, forming cyclic phosphate products from both major substrates, e.g. 1-palmitoyl-sn-glycero-2,3-cyclic-phosphate. Cyclic phosphates have vastly different biological properties from their monoester counterparts, and they may be relevant to the pathology of brown spider envenomation
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
N-lauroyl-D-erythro-sphingosylphosphorylcholine + H2O
lauroyl ceramide-1-phosphate + choline
-
-
-
-
?
sphingomyelin + H2O
ceramide phosphate + choline
-
-
-
-
?
additional information
?
-
-
the recombinant protein rLIPLD1 shows hydrolytic activity on sphingomyelin and in vitro hemolytic activity on human red blood cells, whereas rLIPLD2 is inactive
-
-
?
additional information
?
-
-
the spider venom enzyme cleaves the substrates sphingomyelin and lysophosphatidylcholine in mammalian tissues, releasing the choline head group
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
Mg2+
Mg2+-ion-dependent acid-base mechanism which involves two histidines
Mg2+
-
substrate binding and/or transition state are stabilized by a Mg2+ ion, which is coordinated by Glu32, Asp34, Asp91 and solvent molecules
Mg2+
-
required, residue W256 is capable of coordinating the binding of the Mg2+ ion, along with being one of the negatively charged amino acids which form part of the catalytic pocket
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4-bromo-N-[(E)-(2-methyl-1H-indol-3-yl)methyleneamino]benzenesulfonamide
-
uncompetitive inhibitor
4-methyl-3-oxo-2-(3-pyridylmethylene)benzo[3,4-b]furan-6-yl 4-chloro-benzenesulfonate
-
mixed-type inhibitor
6-amino-2-((4-cyanobenzyl)thio)pyrimidin-4-yl 4-methylbenzenesulfonate
-
uncompetitive inhibitor
additional information
-
enzyme activity is blocked by the anti-loxoscelic antivenom
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
kinetics of enzyme activity on large unilamellar vesicles, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.004
sphingomyelin
crude enzyme, in HEPES-buffered saline at 37°C
0.0175
sphingomyelin
recombinant enzyme SMase II, in HEPES-buffered saline at 37°C
0.004
sphingomyelin
crude enzyme, in HEPES-buffered saline at 37°C
0.0065
sphingomyelin
recombinant enzyme SMase I, in HEPES-buffered saline at 37°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00049
4-bromo-N-[(E)-(2-methyl-1H-indol-3-yl)methyleneamino]benzenesulfonamide
-
at 37°C, pH not specified in the publication
0.00059
4-methyl-3-oxo-2-(3-pyridylmethylene)benzo[3,4-b]furan-6-yl 4-chloro-benzenesulfonate
-
at 37°C, pH not specified in the publication
0.00054
6-amino-2-((4-cyanobenzyl)thio)pyrimidin-4-yl 4-methylbenzenesulfonate
-
at 37°C, pH not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
additional information
-
highly conserved amino acids of the glycerophosphoryl diester phosphodiesterase domain of the recombinant enzyme interact with the substrate sphingomyelin and are involved in substrate recognition. Residues D259 and S262 form part of the catalytic pocket, and they have an important role in substrate recognition and maintenance of the electronegative net charge which sustains the interaction with sphingomyelin
physiological function
-
toxin phospholipases-D in the venom of Loxosceles spiders is the main responsible for local and systemic effects observed in the loxoscelism
physiological function
-
the activity of sphingomyelinase D is clearly influenced by the supramolecular organization of its substrate in membranes and, in situ ceramide-1-phosphate generation by enzymatic activity profoundly alters the lateral structure and morphology of the target membranes
physiological function
-
in loxoscelism, the enzyme increases the expression/secretion of matrix metalloproteinases MMP2 and MMP9 and also stimulates the expression of MMP7 (matrilysin-1), which is associated with keratinocyte cell death
physiological function
-
the enzyme is responsible for the dermonecrosis and systemic effects observed in loxoscelism
physiological function
-
the reaction products of the enzyme promote cell migration and inflammation
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A311_LOXLA
311
0
34874
Swiss-Prot
Secretory Pathway (Reliability: 1)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapour-diffusion method. Crystal structure of the sulfate free enzyme determined at 1.85 A resolution. The metal ion is tetrahedrally coordinated instead of the trigonal-bipyramidal coordination observed in the sulfate bound form
hanging drop vapor diffusion method. crystal structure determined ar 1.75 A resolution using the quick cryo-soaking technique. The enzyme folds as an (alpha/beta)8 barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D259G
-
site-directed mutagenesis, the mutant shows highly reduced sphingomyelinase and hemolytic activity compared to the wild type enzyme, the interaction with sphingomyelin is strongly reduced
D269G
-
site-directed mutagenesis, the mutant shows reduced sphingomyelinase, but unaltered hemolytic activity compared to the wild type enzyme
S257A
-
site-directed mutagenesis, the mutant shows reduced sphingomyelinase, but unaltered hemolytic activity compared to the wild type enzyme
S262A
-
site-directed mutagenesis, the mutant shows reduced sphingomyelinase and hemolytic activity compared to the wild type enzyme
W256S
-
site-directed mutagenesis, the mutant shows reduced sphingomyelinase and hemolytic activity compared to the wild type enzyme, the interaction with sphingomyelin is strongly reduced
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His-tagged recombinant enzyme from Escherichia coli strain BL21(lDE3) by nickel affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
isozymes LIPLD1 and LIPLD2, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, expression in Escherichia coli strain BL21 (DE3)
-
recombinant expression of N-terminally His-tagged recombinant enzyme in Escherichia coli strain BL21(lDE3)
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
recombinant SMase D can replace venom for anti-venom production and therapy
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Van Meeteren, L.A.; Frederiks, F.; Giepmans, B.N.G.; Pedrosa, M.F.F.; Billington, S.J.; Jost, B.H.; Tambourgi, D.V.; Moolenaar, W.H.
Spider and bacterial sphingomyelinases D target cellular lysophosphatidic acid receptors by hydrolyzing lysophosphatidylcholine
J. Biol. Chem.
279
10833-10836
2004
Corynebacterium pseudotuberculosis, Loxosceles laeta
Murakami, M.T.; Fernandes-Pedrosa, M.F.; de Andrade, S.A.; Gabdoulkhakov, A.; Betzel, C.; Tambourgi, D.V.; Arni, R.K.
Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases
Biochem. Biophys. Res. Commun.
342
323-329
2006
Loxosceles laeta (Q8I914)
Murakami, M.T.; Fernandes-Pedrosa, M.F.; Tambourgi, D.V.; Arni, R.K.
Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D
J. Biol. Chem.
280
13658-13664
2005
Loxosceles laeta
Olvera, A.; Ramos-Cerrillo, B.; Estevez, J.; Clement, H.; de Roodt, A.; Paniagua-Solis, J.; Vazquez, H.; Zavaleta, A.; Arruz, M.S.; Stock, R.P.; Alagon, A.
North and South American Loxosceles spiders: development of a polyvalent antivenom with recombinant sphingomyelinases D as antigens
Toxicon
48
64-74
2006
Loxosceles boneti (Q5YD76), Loxosceles boneti, Loxosceles laeta (Q1KY80), Loxosceles laeta, Loxosceles reclusa (Q5YD75), Loxosceles reclusa
de Almeida, D.M.; Fernandes-Pedrosa, M.d.e..F.; de Andrade, R.M.; Marcelino, J.R.; Gondo-Higashi, H.; de Azevedo, I.d.e..L.; Ho, P.L.; van den Berg, C.; Tambourgi, D.V.
A new anti-loxoscelic serum produced against recombinant sphingomyelinase D: results of preclinical trials
Am. J. Trop. Med. Hyg.
79
463-470
2008
Loxosceles gaucho, Loxosceles intermedia (P0CE81), Loxosceles intermedia (P0CE83), Loxosceles intermedia, Loxosceles laeta (Q8I914), Loxosceles laeta
Binford, G.J.; Bodner, M.R.; Cordes, M.H.; Baldwin, K.L.; Rynerson, M.R.; Burns, S.N.; Zobel-Thropp, P.A.
Molecular evolution, functional variation, and proposed nomenclature of the gene family that includes sphingomyelinase D in sicariid spider venoms
Mol. Biol. Evol.
26
547-566
2009
Ixodes scapularis (Q202J4), Loxosceles amazonica, Loxosceles apachea, Loxosceles arizonica (Q7Z1Y7), Loxosceles deserta, Loxosceles hirsuta, Loxosceles intermedia (P0CE81), Loxosceles intermedia (P0CE83), Loxosceles laeta (Q1KY79), Loxosceles laeta (Q1KY80), Loxosceles reclusa (P0CE78), Loxosceles rufescens, Loxosceles sabina, Loxosceles spadicea, Loxosceles speluncarum, Loxosceles spinulosa, Loxosceles vonwredei, no activity in Drymusa capensis, no activity in Drymusa dinora, no activity in Drymusa serrana, no activity in Sicarius peruensis, no activity in Sicarius rugosus, no activity in Sicarius rupestris, no activity in Sicarius terrosus, Sicarius albospinosus, Sicarius damarensis, Sicarius dolichocephalus, Sicarius hahni, Sicarius patagonicus
de Santi Ferrara, G.I.; Fernandes-Pedrosa, M.D.; Junqueira-de-Azevedo, I.D.; Goncalves-de-Andrade, R.M.; Portaro, F.C.; Manzoni-de-Almeida, D.; Murakami, M.T.; Arni, R.K.; van den Berg, C.W.; Ho, P.L.; Tambourgi, D.V.
SMase II, a new sphingomyelinase D from Loxosceles laeta venom gland: Molecular cloning, expression, function and structural analysis
Toxicon
53
743-753
2009
Loxosceles laeta (Q8I912), Loxosceles laeta (Q8I914), Loxosceles laeta
Catalan, A.; Cortes, W.; Sagua, H.; Gonzalez, J.; Araya, J.E.
Two new phospholipase D isoforms of Loxosceles laeta: Cloning, heterologous expression, functional characterization, and potential biotechnological application
J. Biochem. Mol. Toxicol.
25
393-403
2011
Loxosceles laeta
Gomes, M.T.; Guimaraes, G.; Frezard, F.; Kalapothakis, E.; Minozzo, J.C.; Chaim, O.M.; Veiga, S.S.; Oliveira, S.C.; Chavez-Olortegui, C.
Determination of sphingomyelinase-D activity of Loxosceles venoms in sphingomyelin/cholesterol liposomes containing horseradish peroxidase
Toxicon
57
574-579
2011
Loxosceles gaucho, Loxosceles intermedia, Loxosceles laeta, Loxosceles similis, no activity in Bothrops jararaca, no activity in Crotalus durissus, no activity in Lachesis muta, no activity in Micrurus frontalis, no activity in Phoneutria nigriventer, no activity in Tityus serrulatus
Stock, R.P.; Brewer, J.; Wagner, K.; Ramos-Cerrillo, B.; Duelund, L.; Jernsh?j, K.D.; Olsen, L.F.; Bagatolli, L.A.
Sphingomyelinase D activity in model membranes: structural effects of in situ generation of ceramide-1-phosphate
PLoS ONE
7
e36003
2012
Loxosceles laeta
Lajoie, D.M.; Zobel-Thropp, P.A.; Kumirov, V.K.; Bandarian, V.; Binford, G.J.; Cordes, M.H.
Phospholipase D toxins of brown spider venom convert lysophosphatidylcholine and sphingomyelin to cyclic phosphates
PLoS ONE
8
e72372
2013
Loxosceles arizonica (Q4ZFU2), Loxosceles laeta, Loxosceles reclusa
Catalan, A.; Cortes, W.; Munoz, C.; Araya, J.E.
Tryptophan and aspartic acid residues present in the glycerophosphoryl diester phosphodiesterase (GDPD) domain of the Loxosceles laeta phospholipase D are essential for substrate recognition
Toxicon
81
43-47
2014
Loxosceles laeta
Pedroso, A.; Matioli, S.R.; Murakami, M.T.; Pidde-Queiroz, G.; Tambourgi, D.V.
Adaptive evolution in the toxicity of a spiders venom enzymes
BMC Evol. Biol.
15
290
2015
Arcanobacterium haemolyticum, Corynebacterium pseudotuberculosis, Ixodes scapularis, Loxosceles adelaida, Loxosceles aff. spinulosa GJB-2008, Loxosceles amazonica, Loxosceles apachea, Loxosceles arizonica, Loxosceles boneti, Loxosceles cf. spinulosa GJB-2008, Loxosceles deserta, Loxosceles gaucho, Loxosceles hirsuta, Loxosceles intermedia, Loxosceles laeta, Loxosceles reclusa, Loxosceles rufescens, Loxosceles sabina, Loxosceles similis, Loxosceles sp. 4 GJB-2008, Loxosceles spadicea, Loxosceles spinulosa, Loxosceles variegata, Rhipicephalus pulchellus, Sicarius albospinosus, Sicarius damarensis, Sicarius patagonicus, Sicarius peruensis, Sicarius terrosus
Lopes, P.H.; Murakami, M.T.; Portaro, F.C.V.; Mesquita Pasqualoto, K.F.; van den Berg, C.; Tambourgi, D.V.
Targeting Loxosceles spider sphingomyelinase D with small-molecule inhibitors as a potential therapeutic approach for loxoscelism
J. Enzyme Inhib. Med. Chem.
34
310-321
2019
Loxosceles laeta
Correa, M.A.; Okamoto, C.K.; Goncalves-de-Andrade, R.M.; van den Berg, C.W.; Tambourgi, D.V.
Sphingomyelinase D from Loxosceles laeta venom induces the expression of MMP7 in human keratinocytes contribution to dermonecrosis
PLoS ONE
11
e0153090
2016
Loxosceles laeta
Rivera, I.G.; Ordonez, M.; Presa, N.; Gomez-Larrauri, A.; Simon, J.; Trueba, M.; Gomez-Munoz, A.
Sphingomyelinase D/ceramide 1-phosphate in cell survival and inflammation
Toxins
7
1457-1466
2015
Arcanobacterium haemolyticum, Corynebacterium pseudotuberculosis, Corynebacterium ulcerans, Loxosceles arizonica, Loxosceles gaucho, Loxosceles intermedia, Loxosceles laeta, Loxosceles reclusa, Loxosceles rufescens, Photobacterium damselae subsp. damselae
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