2PZ0
Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
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) |
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) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | PLC-like phosphodiesterases | 8060279 | 3000615 | SCOP2B (2022-06-29) |
B | SCOP2 Family | Glycerophosphoryl diester phosphodiesterase | 8060278 | 4000418 | SCOP2 (2022-06-29) |
B | SCOP2 Superfamily | PLC-like phosphodiesterases | 8060279 | 3000615 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | PF03009 | e2pz0A1 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: PF03009 | ECOD (1.6) |
B | PF03009 | e2pz0B1 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: PF03009 | 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) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
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 |
---|---|---|---|---|
Glycerophosphoryl diester phosphodiesterase | - |
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR030395 | Glycerophosphodiester phosphodiesterase domain | Domain | |
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 |
---|---|---|---|
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 | |