2F9R
Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | GDPD_2 | e2f9rA1 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: GDPD_2 | ECOD (1.6) |
B | GDPD_2 | e2f9rB1 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: GDPD_2 | ECOD (1.6) |
C | GDPD_2 | e2f9rC1 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: GDPD_2 | ECOD (1.6) |
D | GDPD_2 | e2f9rD1 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: GDPD_2 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.20.20.190 | Alpha Beta | Alpha-Beta Barrel | TIM Barrel | Phosphatidylinositol (PI) phosphodiesterase | CATH (4.3.0) |
B | 3.20.20.190 | Alpha Beta | Alpha-Beta Barrel | TIM Barrel | Phosphatidylinositol (PI) phosphodiesterase | CATH (4.3.0) |
C | 3.20.20.190 | Alpha Beta | Alpha-Beta Barrel | TIM Barrel | Phosphatidylinositol (PI) phosphodiesterase | CATH (4.3.0) |
D | 3.20.20.190 | Alpha Beta | Alpha-Beta Barrel | TIM Barrel | Phosphatidylinositol (PI) phosphodiesterase | CATH (4.3.0) |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
---|---|---|---|---|
Sphingomyelinase D 1 |
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InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
sphingomyelin phosphodiesterase D (Class I) M-CSA #242 | Sphingomyelinase D (SMase D), isolated from Loxosceles laeta, catalyses the hydrolysis of sphingomyelin to ceramide 1-phosphate (C1P) and choline, and the hydrolysis of lysophosphatidyl choline to lysophosphatidic acid (LPA) and choline. This enzyme belongs to class I of the SMase D enzymes. SMase D is a component of Loxosceles spider venom and and is the principle toxin causing dermonecrosis, acute renal failure, platelet aggregation and systemic intravascular haemolysis. SMase D activity is not found anywhere else in the animal kingdom but some pathogenic bacteria, such as Corynebacterium pseudotuberculosis, produce a similar enzyme as an exotoxin. This enzyme belongs to the arthropod phospholipase D family, Class I subfamily. In addition to hydrolysing sphingomyelin, the enzyme can hydrolyse lysophosphatidyl choline to lysophosphatidic acid and choline. | Defined by 11 residues: HIS:B-12GLU:B-32ASP:B-34HIS:B-47GLY:B-48ASP:B-52ASP:B-91LYS:B-93TRP:B-230ASP:B-233ASN:B-252 | EC: 3.1.4.41 (PDB Primary Data) EC: 4.6.1 (UniProt) |