Information on EC 3.1.4.41 - sphingomyelin phosphodiesterase D

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
3.1.4.41
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RECOMMENDED NAME
GeneOntology No.
sphingomyelin phosphodiesterase D
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
sphingomyelin + H2O = ceramide phosphate + choline
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis
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hydrolysis of phosphoric ester
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Sphingolipid metabolism
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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 hide
54992-31-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Streptococcus hemolyticum
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
Loxosceles sp.
no activity in Bothrops jararaca
venom
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-
Manually annotated by BRENDA team
no activity in Crotalus durissus
venom
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-
Manually annotated by BRENDA team
no activity in Ctenus captiosus
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-
-
Manually annotated by BRENDA team
no activity in Diguetia canites
-
-
-
Manually annotated by BRENDA team
no activity in Drymusa capensis
-
-
-
Manually annotated by BRENDA team
no activity in Drymusa dinora
-
-
-
Manually annotated by BRENDA team
no activity in Drymusa serrana
-
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Manually annotated by BRENDA team
no activity in Kulkania arizonica
-
-
-
Manually annotated by BRENDA team
no activity in Lachesis muta
venom
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-
Manually annotated by BRENDA team
no activity in Leptoneta oasa
-
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-
Manually annotated by BRENDA team
no activity in Micrurus frontalis
venom
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Manually annotated by BRENDA team
no activity in Phoneutria nigriventer
venom
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-
Manually annotated by BRENDA team
no activity in Plectreurys tristis
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-
Manually annotated by BRENDA team
no activity in Scytodes perfecta
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Manually annotated by BRENDA team
no activity in Sicarius peruensis
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Manually annotated by BRENDA team
no activity in Sicarius rugosus
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Manually annotated by BRENDA team
no activity in Sicarius rupestris
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-
Manually annotated by BRENDA team
no activity in Sicarius terrosus
-
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Manually annotated by BRENDA team
no activity in Tityus serrulatus
venom
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Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Sicarius testaceus
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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the enzyme belongs to the the family of phospholipases D, PLD
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1-O-hexadecylglycero-3-phosphocholine + H2O
choline + 1-O-hexadecylglycero-3-phosphate
show the reaction diagram
1-octanoyl-2-hydroxy-sn-glycero-3-phosphocholine + H2O
1-octanoyl-sn-glycero-2,3-cyclic-phosphate + choline
show the reaction diagram
1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine + H2O
1-palmitoyl-sn-glycero-2,3-cyclic-phosphate + choline
show the reaction diagram
2-lysophosphatidylcholine + H2O
2-lysophosphatidate + choline
show the reaction diagram
2-lysophosphatidylcholine + H2O
choline + 2-lysophosphatidate
show the reaction diagram
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-
-
-
?
2-lysophosphatidylcholine + H2O
lysophosphatidic acid + choline
show the reaction diagram
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-
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?
L-alpha-[palmitoyl-1]lysophosphatidylcholine + H2O
?
show the reaction diagram
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-
-
-
?
lysophosphatidylcholine + H2O
lysophosphatidic acid + choline
show the reaction diagram
N-lauroyl-D-erythro-sphingosylphosphorylcholine + H2O
lauroyl ceramide-1-phosphate + choline
show the reaction diagram
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-
-
-
?
phosphatidylcholine
?
show the reaction diagram
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-
-
-
?
phosphatidylcholine + H2O
phosphatidic acid + choline
show the reaction diagram
phosphatidylethanolamine + H2O
?
show the reaction diagram
-
-
-
-
?
sphingomyelin + H2O
ceramide 1-phosphate + choline
show the reaction diagram
sphingomyelin + H2O
ceramide phosphate + choline
show the reaction diagram
sphingomyelin + H2O
ceramide-1-phosphate + choline
show the reaction diagram
sphingomyelin + H2O
choline + ceramide 1-phosphate
show the reaction diagram
sphingomyelin + H2O
choline + ceramide phosphate
show the reaction diagram
sphingomyelin + H2O
N-acylsphingosylphosphate + choline
show the reaction diagram
trinitrophenylaminolauric acid sphingomyelin + H2O
choline + ?
show the reaction diagram
colour reaction for analysis of sphingomyelinase activity
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2-lysophosphatidylcholine + H2O
2-lysophosphatidate + choline
show the reaction diagram
2-lysophosphatidylcholine + H2O
choline + 2-lysophosphatidate
show the reaction diagram
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-
-
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?
2-lysophosphatidylcholine + H2O
lysophosphatidic acid + choline
show the reaction diagram
K9USW8
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?
N-lauroyl-D-erythro-sphingosylphosphorylcholine + H2O
lauroyl ceramide-1-phosphate + choline
show the reaction diagram
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-
-
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?
sphingomyelin + H2O
ceramide 1-phosphate + choline
show the reaction diagram
sphingomyelin + H2O
ceramide phosphate + choline
show the reaction diagram
sphingomyelin + H2O
choline + ceramide 1-phosphate
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
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required for activity
Co2+
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dependent on divalent cations
Mn2+
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dependent on divalent cations
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
diethyldicarbonate
0.02-0.1 mM, complete inhibition, sphingomyelinase P1; 0.02-0.1 mM, complete inhibitionsphingomyelinase P2
phosphatidylinositol-3,5-bisphosphate
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additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
phosphatidylserine
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stimulates
serum amyloid protein
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the only plasma component required by the enzyme for the in vitro-activation of human platelets
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.022 - 0.044
1-O-hexadecylglycero-3-phosphocholine
8.3
lysophosphatidylcholine
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0.02 - 6.2
sphingomyelin
additional information
additional information
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kinetics of enzyme activity on large unilamellar vesicles, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.004 - 0.118
sphingomyelin
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
54.3
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membrane-associated enzyme, pH 7.5, 36.5C
56.8
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isoform 1
84.3
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soluble enzyme, pH 7.5, 36.5C
228.2
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isoform 2
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 - 10
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activity range
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
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assay at
36.5
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assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14500
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sedimentation equilibrium centrifugation
32000
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4 * 32000, SDS-PAGE
32760
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mass spectrometry
34000
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SDS-PAGE
35000
His6-tagged protein Smase II, SDS-PAGE; His6-tagged protein Smase II, SDS-PAGE
52000
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gel filtration
64000 - 70000
69000
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SDS-PAGE
additional information
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32000-35000 Da, SDS-PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
tetramer
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4 * 32000, SDS-PAGE
additional information
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structure molecular modeling, overview
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, hanging drop vapour diffusion method, mixxing of 0.001 ml of 15 mg/ml protein in phosphate buffer, pH 7.0, with 0.001 ml reservoir solution containing 0.1 M Tris-HCl, pH 8.2, 22% PEG 10000, equilibration against 0.5 ml reservoir solution, 18C, X-ray diffraction structure determination and anaysis at 2.6 A resolution
purified PLD, sitting drop vapor diffusion method, 0.002 ml of 17 mg/ml protein solution is mixed with 0.002 ml of reservoir solution containing 0.1 M Tris-HCl, pH 7.5, 40% v/v PEG 200, and equilibration over 1 ml reservoir solution, 18C, X-ray diffraction structure determination and analysis at 1.7 A resolution
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purified recombinant wild-type and H12A mutant enzymes, 0.002 ml of protein solution containing 17 mg/ml wild type enzyme and 9 mg/ml H12A mutant, respectively, are mixed with 0.002 ml of reservoir solution containing 0.1 M Tris-HCl, pH 7.5, 40% v/v PEG 200 for the wild-type enzyme, and 0.1 M Tris-HCl, pH 7.5 and 35% v/v PEG 200 for the H12A mutant, equilibration over 1 ml reservoir solution, X-ray diffraction structure determination and analysis at 1.95 and 1.6 A resolution, respectively
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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
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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
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
treatment of the venom with hyperbaric oxygen does not inactivate the enzyme activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
metal affinity chromatography
Ni2+-chelating Sepharose column chromatography; Ni2+-chelating Sepharose column chromatography
recombinant enzme from Escherichia coli strain BL21 Star(DE3)pLysS by affinity chromatography
recombinant His6-tagged wild-type and mutant H12A phospholipase Ds from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
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recombinant N-terminally His-tagged recombinant enzyme from Escherichia coli strain BL21(lDE3) by nickel affinity chromatography
reverse phase chromatography
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using Ni-NTA chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme expression in Escherichia coli strain BL21(DE3)pLysS
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evolutionary insights from cDNA sequences and gene structure
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expressed as a His-tagged fusion protein
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expressed in Escherichia coli; expressed in Escherichia coli
expression in Escherichia coli
expression of His6-tagged wild-type and mutant H12A phospholipase Ds in Escherichia coli strain BL21(DE3)
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gene LiD1, expression in Escherichia coli strain BL21(DE3)
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isozymes LIPLD1 and LIPLD2, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, expression in Escherichia coli strain BL21 (DE3)
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LiD1 cDNA was subcloned in pET11a and expressed in Escherichia coli, no sphingomyelinase activity found
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recombinant expression in Escherichia coli strain BL21 Star(DE3)pLysS
recombinant expression of N-terminally His-tagged recombinant enzyme in Escherichia coli strain BL21(lDE3)
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H47N
inactive mutant
D259G
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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
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site-directed mutagenesis, the mutant shows reduced sphingomyelinase, but unaltered hemolytic activity compared to the wild type enzyme
H47N
-
inactive mutant
S257A
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site-directed mutagenesis, the mutant shows reduced sphingomyelinase, but unaltered hemolytic activity compared to the wild type enzyme
S262A
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site-directed mutagenesis, the mutant shows reduced sphingomyelinase and hemolytic activity compared to the wild type enzyme
W256S
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site-directed mutagenesis, the mutant shows reduced sphingomyelinase and hemolytic activity compared to the wild type enzyme, the interaction with sphingomyelin is strongly reduced
H47N
-
inactive mutant
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
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use of enzyme as probe of membrane sphingomyelin
medicine