2ZKM | pdb_00002zkm

Crystal Structure of Phospholipase C Beta 2

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth X]	d2zkmx1	All alpha proteins	EF Hand-like	EF-hand	EF-hand modules in multidomain proteins	Phospholipase C-beta-2	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth X]	d2zkmx2	All beta proteins	C2 domain-like	C2 domain (Calcium/lipid-binding domain, CaLB)	PLC-like (P variant)	Phospholipase C-beta-2	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth X]	d2zkmx3	All beta proteins	PH domain-like barrel	PH domain-like	Pleckstrin-homology domain (PH domain)	Phospholipase C-beta-2	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth X]	d2zkmx4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLC-like phosphodiesterases	Mammalian PLC	Phospholipase C-beta-2	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth X]	SCOP2 Family	EF-hand modules in multidomain proteins	8026226	4000949	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Family	PLC-like (P variant)	8026228	4002218	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Family	Pleckstrin-homology domain (PH domain)	8026229	4002395	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Family	Mammalian PLC	8026230	4003332	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	EF-hand	8038605	3001983	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	C2 domain (calcium/lipid-binding domain, calb)	8038607	3000965	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	PH domain-like	8038608	3000134	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	PLC-like phosphodiesterases	8038609	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 [auth X]		e2zkmX1	A: PH domain-like	X: PH domain-like	H: PH domain-like	T: PH	F:	ECOD (20:10:01)
A [auth X]		e2zkmX3	A: Immunoglobulin-like beta-sandwich	X: C2 domain	H: C2 domain	T: C2	F:	ECOD (20:10:01)
A [auth X]		e2zkmX4	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: PI-PLC-Y,PI-PLC-X	F:	ECOD (20:10:01)
A [auth X]		e2zkmX5	A: alpha/beta-Hammerhead/Barrel-sandwich hybrid	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: Single hybrid motif	T: EF-hand_like	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth X]	2.30.29.240	Mainly Beta	Roll	PH-domain like		CATH (4.3.0)
A [auth X]	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
A [auth X]	3.20.20.190	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphatidylinositol (PI) phosphodiesterase	CATH (4.3.0)
A [auth X]	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 [auth X]	PF22631	Phosphoinositide phospholipase C beta1-4-like EF-hand domain (PLCB1-4-like_EFh)	Phosphoinositide phospholipase C beta1-4-like EF-hand domain	This entry represents the first EF-hand domain found in 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1-4 (PLCB1-4) from human and related proteins. PLC-beta isoforms mediate the production of the second messenger molecules diacylgly ...	This entry represents the first EF-hand domain found in 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1-4 (PLCB1-4) from human and related proteins. PLC-beta isoforms mediate the production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) to propagate signals for several physiological responses [1-5].	Domain
A [auth X]	PF17787	PH domain (PH_14)	PH domain	This entry corresponds to the PH domain found at the N-terminus of phospholipase C enzymes [1].	Domain
A [auth X]	PF00387	Phosphatidylinositol-specific phospholipase C, Y domain (PI-PLC-Y)	Phosphatidylinositol-specific phospholipase C, Y domain	-	Family
A [auth X]	PF00388	Phosphatidylinositol-specific phospholipase C, X domain (PI-PLC-X)	Phosphatidylinositol-specific phospholipase C, X domain	-	Family
A [auth X]	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 [auth X]	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2	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 phospholipid binding lipid binding protein-containing complex binding G-protein beta/gamma-subunit complex binding	phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process primary metabolic process phosphorus metabolic process lipid metabolic process multicellular organismal process system process nervous system process response to stimulus detection of chemical stimulus involved in sensory perception of bitter taste detection of chemical stimulus involved in sensory perception of taste phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process primary metabolic process phosphorus metabolic process lipid metabolic process multicellular organismal process system process nervous system process response to stimulus detection of chemical stimulus involved in sensory perception of bitter taste detection of chemical stimulus involved in sensory perception of taste detection of stimulus sensory perception of chemical stimulus sensory perception sensory perception of taste response to chemical detection of chemical stimulus sensory perception of bitter taste detection of stimulus involved in sensory perception detection of chemical stimulus involved in sensory perception cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication phosphatidylinositol-mediated signaling signal transduction lipid catabolic process catabolic process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis cell migration cell motility locomotion phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway calcium ion transmembrane import into cytosol transport monoatomic ion transmembrane transport establishment of localization calcium ion transport metal ion transport monoatomic cation transmembrane transport transmembrane transport release of sequestered calcium ion into cytosol localization monoatomic ion transport monoatomic cation transport calcium ion transmembrane transport phosphatidylinositol metabolic process glycerophospholipid metabolic process glycerolipid metabolic process	membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle neuronal dense core vesicle cytosol protein-containing complex G-protein beta/gamma-subunit complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X]	IPR028403	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2, catalytic domain	Domain
A [auth X]	IPR016280	Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta	Family
A [auth X]	IPR001711	Phospholipase C, phosphatidylinositol-specific, Y domain	Domain
A [auth X]	IPR000008	C2 domain	Domain
A [auth X]	IPR000909	Phosphatidylinositol-specific phospholipase C, X domain	Domain
A [auth X]	IPR046969	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2, EF-hand domain	Domain
A [auth X]	IPR011992	EF-hand domain pair	Homologous Superfamily
A [auth X]	IPR053945	Phosphoinositide phospholipase C beta 1-4-like, EF-hand domain	Domain
A [auth X]	IPR001192	Phosphoinositide phospholipase C family	Family
A [auth X]	IPR042531	Phospholipase C-beta, C-terminal domain superfamily	Homologous Superfamily
A [auth X]	IPR017946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily	Homologous Superfamily
A [auth X]	IPR014815	Phospholipase C-beta, C-terminal domain	Domain
A [auth X]	IPR035892	C2 domain superfamily	Homologous Superfamily
A [auth X]	IPR037862	PLC-beta, PH domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth X]	Pharos: Q00722	chronic kidney disease malignant mesothelioma subependymal giant cell astrocytoma heart disease myocardial infarction lung carcinoma psoriasis

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.