1DJX | pdb_00001djx

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-1,4,5-TRISPHOSPHATE

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)
A	d1djxa1	All alpha proteins	EF Hand-like	EF-hand	EF-hand modules in multidomain proteins	Phosphoinositide-specific phospholipase C, isozyme D1 (PLC-D!)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1djxa2	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	PLC-like (P variant)	PI-specific phospholipase C isozyme D1 (PLC-D1), C-terminal domain	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1djxa3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Mammalian PLC	Phospholipase C isozyme D1 (PLC-D1)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1djxb1	All alpha proteins	EF Hand-like	EF-hand	EF-hand modules in multidomain proteins	Phosphoinositide-specific phospholipase C, isozyme D1 (PLC-D!)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1djxb2	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	PLC-like (P variant)	PI-specific phospholipase C isozyme D1 (PLC-D1), C-terminal domain	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1djxb3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Mammalian PLC	Phospholipase C isozyme D1 (PLC-D1)	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	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	8043839	3000615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040702	3000965	SCOP2B (2022-06-29)
B	SCOP2 Family	EF-hand modules in multidomain proteins	8024997	4000949	SCOP2 (2022-06-29)
B	SCOP2 Family	PLC-like (P variant)	8028323	4002218	SCOP2 (2022-06-29)
B	SCOP2 Family	Mammalian PLC	8031461	4003332	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	EF-hand	8037376	3001983	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8040702	3000965	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PLC-like phosphodiesterases	8043839	3000615	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e1djxA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
A	e1djxA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PF27526	F:	ECOD (20:10:01)
A	e1djxA3	A: UBC-like	X: UBC-like	H: Concanavalin A-like lectins/glucanases	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)
B	e1djxB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
B	e1djxB3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PF27526	F:	ECOD (20:10:01)
B	e1djxB4	A: UBC-like	X: UBC-like	H: Concanavalin A-like lectins/glucanases	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
A	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
A	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)
B	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
B	2.60.40.150	Mainly Beta	Sandwich	Immunoglobulin-like	C2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09279	Phosphoinositide-specific phospholipase C, efhand-like (EF-hand_like)	Phosphoinositide-specific phospholipase C, efhand-like	Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme [1].	Domain
A, B	PF00387	Phosphatidylinositol-specific phospholipase C, Y domain (PI-PLC-Y)	Phosphatidylinositol-specific phospholipase C, Y domain	-	Family
A, B	PF00388	Phosphatidylinositol-specific phospholipase C, X domain (PI-PLC-X)	Phosphatidylinositol-specific phospholipase C, X domain	-	Family
A, B	PF00168	C2 domain (C2)	C2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1	phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphatidylinositol phospholipase C activity phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity catalytic activity lipase activity cation binding ion binding binding calcium ion binding phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphatidylinositol phospholipase C activity phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity catalytic activity lipase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding phosphatidylinositol-4,5-bisphosphate phospholipase C activity anion binding phosphatidic acid binding phospholipid binding lipid binding GTPase activating protein binding protein binding phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding phosphatidylinositol binding calcium-dependent phospholipid binding phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity phosphatidylinositol-4,5-bisphosphate phosphatase activity phosphatidylinositol bisphosphate phosphatase activity phosphatase activity phosphatidylinositol phosphate 5-phosphatase activity phosphatidylinositol phosphate phosphatase activity alcohol binding inositol 1,4,5 trisphosphate binding enzyme binding	labyrinthine layer blood vessel development developmental process placenta blood vessel development multicellular organismal process placenta development chordate embryonic development animal organ development labyrinthine layer development embryo development in utero embryonic development vasculature development circulatory system development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching labyrinthine layer blood vessel development developmental process placenta blood vessel development multicellular organismal process placenta development chordate embryonic development animal organ development labyrinthine layer development embryo development in utero embryonic development vasculature development circulatory system development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching anatomical structure development embryonic organ development blood vessel development system development response to stimulus response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound response to metal ion response to calcium ion blood vessel morphogenesis tube development angiogenesis anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication phospholipase C/protein kinase C signal transduction intracellular signaling cassette cellular process signal transduction cellular response to metal ion cellular response to chemical stimulus cellular response to calcium ion lipid catabolic process catabolic process metabolic process primary metabolic process lipid metabolic process phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cell population proliferation regulation of cell population proliferation phosphatidylinositol metabolic process glycerophospholipid metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process glycerolipid metabolic process phosphorus metabolic process response to prostaglandin response to lipid response to prostaglandin F regulation of inositol phosphate biosynthetic process positive regulation of biological process regulation of inositol trisphosphate biosynthetic process alcohol metabolic process inositol phosphate metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of inositol trisphosphate biosynthetic process regulation of small molecule metabolic process positive regulation of biosynthetic process polyol biosynthetic process inositol trisphosphate metabolic process small molecule metabolic process regulation of carbohydrate metabolic process positive regulation of cellular process regulation of biosynthetic process carbohydrate metabolic process polyol metabolic process regulation of alcohol biosynthetic process positive regulation of phosphorus metabolic process small molecule biosynthetic process inositol trisphosphate biosynthetic process carbohydrate biosynthetic process biosynthetic process positive regulation of inositol phosphate biosynthetic process organophosphate biosynthetic process inositol phosphate biosynthetic process alcohol biosynthetic process regulation of phosphorus metabolic process regulation of carbohydrate biosynthetic process positive regulation of carbohydrate metabolic process positive regulation of small molecule metabolic process regulation of metabolic process positive regulation of alcohol biosynthetic process response to aluminum ion monoamine transport regulation of localization nitrogen compound transport transport regulation of catecholamine secretion organic hydroxy compound transport positive regulation of secretion by cell positive regulation of amine transport localization secretion by cell regulation of secretion by cell catecholamine transport positive regulation of secretion signal release norepinephrine transport secretion regulation of transport positive regulation of catecholamine secretion export from cell cell-cell signaling establishment of localization positive regulation of norepinephrine secretion organic cation transport regulation of secretion catecholamine secretion amine transport positive regulation of transport norepinephrine secretion regulation of amine transport regulation of norepinephrine secretion response to stress response to oxygen levels response to abiotic stimulus response to hyperoxia response to increased oxygen levels	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane cytosol membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane cytosol cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001849	Pleckstrin homology domain	Domain
A, B	IPR001711	Phospholipase C, phosphatidylinositol-specific, Y domain	Domain
A, B	IPR000008	C2 domain	Domain
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR000909	Phosphatidylinositol-specific phospholipase C, X domain	Domain
A, B	IPR046975	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1, EF-hand domain	Domain
A, B	IPR002048	EF-hand domain	Domain
A, B	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A, B	IPR015359	Phosphoinositide-specific phospholipase C, EF-hand-like domain	Domain
A, B	IPR001192	Phosphoinositide phospholipase C family	Family
A, B	IPR028391	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1, catalytic domain	Domain
A, B	IPR017946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily	Homologous Superfamily
A, B	IPR035892	C2 domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	phosphoinositide phospholipase C M-CSA #28	Mammalian phospholipase C catalyses the hydrolysis of inositol lipid to inositol 1,4,5 trisphosphate and diacyl glycerol, both of which are important second messengers in Ca(II) signalling pathways. It possesses a Triose phosphate isomerase-like catalytic domain, indicating some homology with triosephosphate isomerase, but catalyses a different reaction by a mechanism more similar to the T1 RNAases.	Defined by 6 residues: HIS:A-179 [auth A-311]ASN:A-180 [auth A-312]GLU:A-209 [auth A-341]ASP:A-211 [auth A-343]HIS:A-224 [auth A-356]GLU:A-258 [auth A-390] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.4.11 (PDB Primary Data) Search M-CSA Motif + EC 3.1.4.11

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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