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Information on EC 3.1.4.12 - sphingomyelin phosphodiesterase and Organism(s) Bacillus cereus and UniProt Accession P09599

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.4 Phosphoric-diester hydrolases
                3.1.4.12 sphingomyelin phosphodiesterase
IUBMB Comments
Has very little activity on phosphatidylcholine.
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This record set is specific for:
Bacillus cereus
UNIPROT: P09599
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Word Map
The taxonomic range for the selected organisms is: Bacillus cereus
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
sphingomyelinase, alpha-toxin, acid sphingomyelinase, smase, neutral sphingomyelinase, asmase, nsmase2, nsmase, n-smase, smpd1, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
neutral sphingomyelinase
-
acid sphingomyelinase
alkaline sphingomyelinase
-
-
-
-
aSMase
Bc-SMase
Beta-hemolysin
-
-
-
-
Beta-toxin
-
-
-
-
bSMase
-
-
Lyso-PAF-PLC
-
-
-
-
N-SMase
-
-
-
-
neutral SMase
-
-
neutral sphingomyelinase
nSMase
phosphodiesterase, sphingomyelin
-
-
-
-
SMase
SMPLC
-
-
-
-
sphingomyelin phosphodiesterase
-
-
-
-
sphingomyelinase
sphingomyelinase C
Sphmase
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a sphingomyelin + H2O = a ceramide + phosphocholine
show the reaction diagram
catalytic mechanism, a number of key residues involved in metal binding and catalysis are conserved in neutral sphingomyelinases, e.g. Glu53, Asp126, Asp295, and His296 are essential, structure-function analysis, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
additional information
-
SMase belongs to the family of interfacial enzymes that carry out processive catalytic turnover at the interface, SMase binds rapidly and avidly to sphingomyelin vesicles and it is fully active as a monomer at the interface
PATHWAY SOURCE
PATHWAYS
-
-, -
SYSTEMATIC NAME
IUBMB Comments
sphingomyelin cholinephosphohydrolase
Has very little activity on phosphatidylcholine.
CAS REGISTRY NUMBER
COMMENTARY hide
9031-54-3
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
sphingomyelin + H2O
N-acylsphingosine + choline phosphate
show the reaction diagram
2-hexadecanoylamino-4-nitrophenylphosphocholine + H2O
2-hexadecanoylamino-4-nitrophenol + choline phosphate
show the reaction diagram
2-n-hexadecanoylamino-4-nitrophenylphosphorylcholine + H2O
2-n-hexadecanoylamino-4-nitrophenol + choline phosphate
show the reaction diagram
-
-
-
-
?
4-nitrophenyl phosphorylcholine + H2O
4-nitrophenol + phosphorylcholine
show the reaction diagram
-
-
-
-
?
a sphingomyelin + H2O
a ceramide + choline phosphate
show the reaction diagram
-
-
-
-
?
a sphingomyelin + H2O
a ceramide + phosphocholine
show the reaction diagram
-
-
a ceramide is an N-acylsphingosine
-
?
hexadecanoyl-p-nitrophenylphosphorylcholine + H2O
hexadecanoyl-p-nitrophenol + choline phosphate
show the reaction diagram
-
-
-
-
?
lysophosphatidylcholine + H2O
1-acylglycerol + choline phosphate
show the reaction diagram
lysophosphatidylcholine + H2O
acylglycerol + choline phosphate
show the reaction diagram
-
-
-
?
p-nitrophenylphosphorylcholine + H2O
choline phosphate + p-nitrophenol
show the reaction diagram
-
-
-
-
?
sphingomyelin + H2O
?
show the reaction diagram
-
-
-
-
?
sphingomyelin + H2O
ceramide + phosphocholine
show the reaction diagram
-
-
-
-
?
sphingomyelin + H2O
N-acylsphingosine + choline phosphate
show the reaction diagram
sphingosylphosphocholine + H2O
sphingosine + choline phosphate
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
sphingomyelin + H2O
N-acylsphingosine + choline phosphate
show the reaction diagram
neutral sphingomyelinases are considered major candidates for mediating the stress-induced production of ceramide, regulation, physiological, and pathological roles of these proteins, overview
-
-
?
a sphingomyelin + H2O
a ceramide + phosphocholine
show the reaction diagram
-
-
a ceramide is an N-acylsphingosine
-
?
sphingomyelin + H2O
?
show the reaction diagram
-
-
-
-
?
sphingomyelin + H2O
ceramide + phosphocholine
show the reaction diagram
-
-
-
-
?
sphingomyelin + H2O
N-acylsphingosine + choline phosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
required by N-SMase for activity, residues Glu53, Asp126, Asp295, and His296 are critical for Mg2+ binding and catalytic activity
Zn2+
Zn2+ binding to the high-affinity site activates the enzyme and, conversely, binding to the low-affinity site inhibits the enzyme
Sr2+
Km: 0.018 mM, activation of sphingomyelinase activity in the order of decreasing efficiency Co2+, Mn2+, Mg2+, Ca2+, Sr2+
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
BeF2
an unusual phosphate analogue
Zn2+
Zn2+ binding to the high-affinity site activates the enzyme and, conversely, binding to the low-affinity site inhibits the enzyme
amitriptyline
-
-
bromoenol lactone
-
-
ceramide
-
feedback inhibition
cetyltrimethylammonium bromide
-
-
chitosan-iron complex FeChi-CH3
-
-
-
Cu2+
-
0.0079 mM, 50% inhibitiion
imipramine
-
-
N-[(2S,3R,4E)-1-(2,2'-bipyridin-6-ylmethoxy)-3-hydroxyoctadec-4-en-2-yl]hexanamide [Mg2+]
-
i.e. RY221B-a, synthesis, binding simulations and docking study, overview
N-[(2S,3R,4E)-3-(2,2'-bipyridin-6-ylmethoxy)-1-hydroxyoctadec-4-en-2-yl]hexanamide
-
i.e. RY221B-b, synthesis, binding simulations and docking study, overview
palmitate
-
a non-substrate lipid belonging to the phospholipase A2 pathway
Triton X-100
-
slight inhibition with 2-hexadecynoylamino-4-nitrophenylphosphorylcholine
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
C2 toxin
-
activates acid but not neutral sphingomyelinase
-
cholesterol
-
sphingomyelinase activity is higher in the cholesterol-induced liquid-ordered phase than in the gel phase
deoxycholate
-
3fold stimulation at concentrations above 0.1%
Detergents
-
-
sodium deoxycholate
-
-
Triton X-100
-
activation with sphingomyelin
additional information
-
the topography of the lipid monolayer surface, through phase connection-disconnection of substrate-enriched or substrate-depleted domains, can dynamically regulate SMase activity
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.034
2-n-hexadecanoylamino-4-nitrophenylphosphorylcholine
-
in presence of Mg2+
11.6
4-nitrophenyl phosphorylcholine
-
-
0.174
hexadecanoyl-p-nitrophenyl phosphorylcholine
-
-
0.038 - 0.565
sphingomyelin
additional information
additional information
-
different SMase kinetic steps are differentially regulated by non-substrate lipids, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5.9
2-hexadecanoylamino-4-nitrophenylphosphocholine
-
37°C, pH 7.5
13
lysophosphatidylcholine
-
37°C, pH 7.5
3.6 - 400
sphingomyelin
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0052
N-[(2S,3R,4E)-1-(2,2'-bipyridin-6-ylmethoxy)-3-hydroxyoctadec-4-en-2-yl]hexanamide [Mg2+]
-
pH and temperature not specified in the publication
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0012
N-[(2S,3R,4E)-1-(2,2'-bipyridin-6-ylmethoxy)-3-hydroxyoctadec-4-en-2-yl]hexanamide [Mg2+]
Bacillus cereus
-
pH and temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.46
-
sphingosylphosphocholine hydrolysis
0.49
-
sphingomyelin hydrolysis
additional information
-
different assay conditions, substrates etc.
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
membrane binding assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
nSMase
SwissProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
nSMase, with a cleavable secretory signal sequence at their N-terminus, is a secretory protein released from cells
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
-
enzyme knockdown reduces Clostridium botulinum C2 toxin-induced cell rounding
physiological function
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PHL1_BACCE
333
0
36949
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23300
-
sedimentation equilibrium centrifugation
24000
-
gel filtration
34000
-
x * 34000, SDS-PAGE
34271
-
x * 34271, deduced from nucleotide sequence
41000
-
x * 41000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
nSMase, crystal structure of nSMase complexed with Ca2+, Co2+, or Mg2+, and structure-function analysis
hanging drop vapor diffusion method, crystal structures of Bc-SMase complexed to the functional metal ions Mg2+, Co2+, or Ca2+ are determined at 1.8 A, 1.8 A, and 1.4 A resolution, respectively
purified recombinant mutant N57A enzyme, hanging drop vapor diffusion method, mixing of 0.002 ml of 10 mg/ml protein in 20 mM Tris-HCl, pH7.0, with 0.002 ml of reservoir solution containing 18% w/v PEG 8000, 0.2 M MgCl2, and 0.1 M sodium cacodylate, pH 6.5, 4°C, X-ray diffraction structure determination and analysis at 2.4 A resolution
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D100A
-
site-directed mutagenesis, mutation in close proximity to Mg2+ at the side-edge, the mutant shows reduced binding to and hydrolysis of sphingomyelin in membranes of sheep erythrocytes or SM-liposomes, similar catalytic activity compared to the wild-type enzyme
E53D
-
5% of wild-type sphingomyelin hydrolyzing activity, E53 acts as an indespensable ligand of Mg2+ essential for catalytic activity
E53Q
-
no sphingomyelin hydrolyzing and no hemolytic activity, E53 acts as an indespensable ligand of Mg2+ essential for catalytic activity
E99A
-
site-directed mutagenesis, mutation in close proximity to Mg2+ at the side-edge, the mutant shows reduced binding to and hydrolysis of sphingomyelin in membranes of sheep erythrocytes or SM-liposomes, similar catalytic activity compared to the wild-type enzyme
F285A
F55A
-
site-directed mutagenesis, the mutation in close proximity to Mg2+ at the side-edge does not affect the enzyme
H151A
H151D
-
no nSMase activity
H151E
-
no nSMase activity
H151F
-
no nSMase activity
H151K
-
no nSMase activity
H151N
-
no nSMase activity
H151Q
-
8.3% of wild-type nSMase activity
H151R
-
no nSMase activity
H151Y
-
no nSMase activity
N57A
-
site-directed mutagenesis, mutation in close proximity to Mg2+ at the side-edge, the mutant shows reduced binding to and hydrolysis of sphingomyelin in membranes of sheep erythrocytes or SM-liposomes, mutant N57A loses the metal ion at the side-edge, similar catalytic activity compared to the wild-type enzyme
W284A
additional information
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 7.5
-
-
135166
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C for 24 h, at pH 6-7.5
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
2200fold
-
recombinant nSMase
-
recombinant SMase
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Bacillus brevis
-
expression in Escherichia coli
-
expression of nSMase in Bacillus brevis 47
-
expression of wild-type and mutant enzymes in Bacillus subtilis strain ISW1214
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Tomita, M.; Taguchi, R.; Ikezawa, H.
Molecular properties and kinetic studies on sphingomyelinase of Bacillus cereus
Biochim. Biophys. Acta
704
90-99
1982
Bacillus cereus
Manually annotated by BRENDA team
Ikezawa, H.; Mori, M.; Ohyabu, T.; Taguchi, R.
Studies on sphingomyelinase of Bacillus cereus. I. Purification and properties
Biochim. Biophys. Acta
528
247-256
1978
Bacillus cereus
Manually annotated by BRENDA team
Yu, B.Z.; Zakim, D.; Jain, M.K.
Processive interfacial catalytic turnover by Bacillus cereus sphingomyelinase on sphingomyelin vesicles
Biochim. Biophys. Acta
1583
122-132
2002
Bacillus cereus
Manually annotated by BRENDA team
Obama, T.; Fujii, S.; Ikezawa, H.; Ikeda, K.; Imagawa, M.; Tsukamoto, K.
His151 and His296 are the acid-base catalytic residues of Bacillus cereus sphingomyelinase in sphingomyelin hydrolysis
Biol. Pharm. Bull.
26
920-926
2003
Bacillus cereus
Manually annotated by BRENDA team
Fanani, M.L.; Hartel, S.; Oliveira, R.G.; Maggio, B.
Bidirectional control of sphingomyelinase activity and surface topography in lipid monolayers
Biophys. J.
83
3416-3424
2002
Bacillus cereus
Manually annotated by BRENDA team
Miura, Y.; Gotoh, E.; Nara, F.; Nishijima, M.; Hanada, K.
Hydrolysis of sphingosylphosphocholine by neutral sphingomyelinases
FEBS Lett.
557
288-292
2004
Bacillus cereus, Homo sapiens
Manually annotated by BRENDA team
Obama, T.; Kan, Y.; Ikezawa, H.; Imagawa, M.; Tsukamoto, K.
Glu-53 of Bacillus cereus sphingomyelinase acts as an indispensable ligand of Mg2+ essential for catalytic activity
J. Biochem.
133
279-286
2003
Bacillus cereus
Manually annotated by BRENDA team
Fanani, M.L.; Maggio, B.
Kinetic steps for the hydrolysis of sphingomyelin by Bacillus cereus sphingomyelinase in lipid monolayers
J. Lipid Res.
41
1832-1840
2000
Bacillus cereus
Manually annotated by BRENDA team
Itoh, F.S.; Yoshida, A.; Higashi, S.; Ikezawa, H.; Ikeda, K.
Activation of sphingomyelinase from Bacillus cereus by Zn2+ hitherto accepted as a strong inhibitor
Arch. Biochem. Biophys.
43
227-236
2005
Bacillus cereus
-
Manually annotated by BRENDA team
Yu, B.Z.; Polenova, T.; Jain, M.K.; Berg, O.G.
Premicellar complexes of sphingomyelinase mediate enzyme exchange for the stationary phase turnover
Biochim. Biophys. Acta
1712
137-151
2005
Bacillus cereus
Manually annotated by BRENDA team
Contreras, F.X.; Sot, J.; Ruiz-Arguello, M.B.; Alonso, A.; Goni, F.M.
Cholesterol modulation of sphingomyelinase activity at physiological temperatures
Chem. Phys. Lipids
130
127-134
2004
Bacillus cereus
Manually annotated by BRENDA team
Nishiwaki, H.; Ito, K.; Otsuki, K.; Yamamoto, H.; Komai, K.; Matsuda, K.
Purification and functional characterization of insecticidal sphingomyelinase C produced by Bacillus cereus
Eur. J. Biochem.
271
601-606
2004
Bacillus cereus
Manually annotated by BRENDA team
Ago, H.; Oda, M.; Takahashi, M.; Tsuge, H.; Ochi, S.; Katunuma, N.; Miyano, M.; Sakurai, J.
Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from bacillus cereus
J. Biol. Chem.
281
16157-16167
2006
Bacillus cereus (P11889), Bacillus cereus
Manually annotated by BRENDA team
Clarke, C.J.; Snook, C.F.; Tani, M.; Matmati, N.; Marchesini, N.; Hannun, Y.A.
The extended family of neutral sphingomyelinases
Biochemistry
45
11247-11256
2006
Helicobacter pylori, Staphylococcus aureus, Rattus norvegicus, Homo sapiens (O60906), Homo sapiens (Q9NY59), Bacillus cereus (P09599), Listeria ivanovii (Q9RLV9), Listeria ivanovii nSMase (Q9RLV9), Helicobacter pylori nSMase, Bacillus cereus nSMase (P09599)
Manually annotated by BRENDA team
De Tullio, L.; Maggio, B.; Hartel, S.; Jara, J.; Fanani, M.L.
The initial surface composition and topography modulate sphingomyelinase-driven sphingomyelin to ceramide conversion in lipid monolayers
Cell Biochem. Biophys.
47
169-177
2007
Bacillus cereus
Manually annotated by BRENDA team
Coll, O.; Morales, A.; Fernandez-Checa, J.C.; Garcia-Ruiz, C.
Neutral sphingomyelinase-induced ceramide triggers germinal vesicle breakdown and oxidant-dependent apoptosis in Xenopus laevis oocytes
J. Lipid Res.
48
1924-1935
2007
Bacillus cereus, Homo sapiens
Manually annotated by BRENDA team
Finnegan, C.M.; Rawat, S.S.; Cho, E.H.; Guiffre, D.L.; Lockett, S.; Merrill, A.H.; Blumenthal, R.
Sphingomyelinase restricts the lateral diffusion of CD4 and inhibits human immunodeficiency virus fusion
J. Virol.
81
5294-5304
2007
Bacillus cereus
Manually annotated by BRENDA team
Walters, M.J.; Wrenn, S.P.
Effect of sphingomyelinase-mediated generation of ceramide on aggregation of low-density lipoprotein
Langmuir
24
9642-9647
2008
Bacillus cereus
Manually annotated by BRENDA team
Marco, C.; Jimenez-Lopez, J.M.; Rios-Marco, P.; Segovia, J.L.; Carrasco, M.P.
Hexadecylphosphocholine alters nonvesicular cholesterol traffic from the plasma membrane to the endoplasmic reticulum and inhibits the synthesis of sphingomyelin in HepG2 cells
Int. J. Biochem. Cell Biol.
41
1296-1303
2009
Bacillus cereus
Manually annotated by BRENDA team
Imagawa, H.; Oda, M.; Takemoto, T.; Yamauchi, R.; Yoshikawa, T.; Yamamoto, H.; Nishizawa, M.; Takahashi, H.; Hashimoto, M.; Yabiku, K.; Nagahama, M.; Sakurai, J.
Synthesis and evaluation of novel phosphate ester analogs as neutral sphingomyelinase inhibitors
Bioorg. Med. Chem. Lett.
20
3868-3871
2010
Bacillus cereus
Manually annotated by BRENDA team
Oda, M.; Takahashi, M.; Tsuge, H.; Nagahama, M.; Sakurai, J.
Role of side-edge site of sphingomyelinase from Bacillus cereus
Biochem. Biophys. Res. Commun.
422
128-132
2012
Bacillus cereus, Bacillus cereus IAM1029
Manually annotated by BRENDA team
Oda, M.; Fujita, A.; Okui, K.; Miyamoto, K.; Shibutani, M.; Takagishi, T.; Nagahama, M.
Bacillus cereus sphingomyelinase recognizes ganglioside GM3
Biochem. Biophys. Res. Commun.
431
164-168
2013
Bacillus cereus, Bacillus cereus IAM1029
Manually annotated by BRENDA team
Caro, C.A.; Lillo, L.; Valenzuela, F.J.; Cabello, G.
Mechanistic characterization and inhibition of sphingomyelinase C over substituted Iron Schiff bases of chitosan adsorbed on glassy carbon electrode
Chem. Biol. Interact.
263
81-87
2017
Bacillus cereus
Manually annotated by BRENDA team
Nagahama, M.; Takehara, M.; Takagishi, T.; Seike, S.; Miyamoto, K.; Kobayashi, K.
Cellular uptake of Clostridium botulinum C2 toxin requires acid sphingomyelinase activity
Infect. Immun.
85
e00966-16
2017
Bacillus cereus
Manually annotated by BRENDA team