2F9R

Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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)
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)
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)

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)
D	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Sphingomyelinase D 1	lyase activity catalytic activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity cation binding ion binding binding metal ion binding small molecule binding toxin activity	lipid catabolic process catabolic process metabolic process primary metabolic process lipid metabolic process biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	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 \| Explore in 3D: M-CSA Motif Definition Up to 10 residues are supported for Structure Motif searching, this motif has 11 residues. EC: 3.1.4.41 (PDB Primary Data) EC: 4.6.1 (UniProt)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.