2PZ0 | pdb_00002pz0

Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2pz0b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	automated matches	automated matches	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)
A	d2pz0a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	automated matches	automated matches	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Glycerophosphoryl diester phosphodiesterase	8060278	4000418	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PLC-like phosphodiesterases	8060279	3000615	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	PLC-like phosphodiesterases	8060279	3000615	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	GDPD	e2pz0B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)
A	GDPD	e2pz0A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: GDPD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
A	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03009	Glycerophosphoryl diester phosphodiesterase family (GDPD)	Glycerophosphoryl diester phosphodiesterase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glycerophosphoryl diester phosphodiesterase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	primary metabolic process metabolic process cellular process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR030395	Glycerophosphodiester phosphodiesterase domain	Domain
A, B	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
A	glycerophosphodiester phosphodiesterase M-CSA #300	Glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol) all of which are are hydrolysed by this enzyme. Although this enzyme will function with Ca(II) ions, it more active with Mg(II) ions.	Defined by 8 residues: HIS:A-17ARG:A-18GLU:A-44ASP:A-46HIS:A-59GLU:A-119LYS:A-121ASP:A-239 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.4.46 (UniProt) Search M-CSA Motif + EC 3.1.4.46

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.