3IBJ | pdb_00003ibj

X-ray structure of PDE2A

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8067455	3000943	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HD-domain/PDEase-like	8067455	3000943	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	YonK	e3ibjB2	A: alpha bundles	X: DP domain	H: DP domain	T: DP domain	F: YonK	ECOD (develop294)
B	MR_MLE_N	e3ibjB4	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: MR_MLE_N	ECOD (develop294)
A	Flavi_glycoprot	e3ibjA1	A: alpha bundles	X: Cystatin-like	H: Cupredoxin-related	T: Cupredoxin-related	F: Flavi_glycoprot	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
B	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
A	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
A	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01590	GAF domain (GAF)	GAF domain	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regul ...	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
A, B	PF00233	3'5'-cyclic nucleotide phosphodiesterase (PDEase_I)	3'5'-cyclic nucleotide phosphodiesterase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	cGMP-dependent 3',5'-cyclic phosphodiesterase	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity 3',5'-cyclic-nucleotide phosphodiesterase activity hydrolase activity cyclic-nucleotide phosphodiesterase activity catalytic activity 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity 3',5'-cyclic-nucleotide phosphodiesterase activity hydrolase activity cyclic-nucleotide phosphodiesterase activity catalytic activity 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding cGMP binding small molecule binding 3',5'-cyclic-AMP phosphodiesterase activity identical protein binding protein binding cation binding magnesium ion binding metal ion binding phosphate ion binding protein homodimerization activity protein dimerization activity adenyl ribonucleotide binding cAMP binding adenyl nucleotide binding TPR domain binding protein domain specific binding transition metal ion binding zinc ion binding 3',5'-cyclic-GMP phosphodiesterase activity	response to peptide response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus regulation of defense response regulation of biological process regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus response to peptide response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus regulation of defense response regulation of biological process regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response ribose phosphate metabolic process ribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process cyclic nucleotide metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleotide catabolic process nucleoside phosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process cyclic purine nucleotide metabolic process primary metabolic process purine-containing compound catabolic process cyclic nucleotide catabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound catabolic process cGMP metabolic process organophosphate metabolic process cGMP catabolic process metabolic process cellular process purine ribonucleotide metabolic process regulation of biosynthetic process regulation of cellular process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of receptor guanylyl cyclase signaling pathway negative regulation of cell communication cell communication negative regulation of cellular process receptor guanylyl cyclase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of cell communication developmental process multicellular organism development multicellular organismal process artery development anatomical structure development aorta development vasculature development blood vessel development system development circulatory system development negative regulation of vascular permeability regulation of vascular permeability system process circulatory system process vascular process in circulatory system regulation of biological quality blood circulation regulation of cellular component organization regulation of organelle organization cellular component organization organelle organization regulation of mitochondrion organization cellular component organization or biogenesis mitochondrion organization positive regulation of vascular permeability myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development mononuclear cell differentiation myeloid cell differentiation cell differentiation monocyte differentiation leukocyte differentiation negative regulation of G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway adenylate cyclase-activating G protein-coupled receptor signaling pathway negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway cellular response to chemical stimulus cellular response to xenobiotic stimulus response to xenobiotic stimulus RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular response to nitrogen compound response to organophosphorus cellular response to cGMP response to oxygen-containing compound response to nitrogen compound response to cGMP response to purine-containing compound cellular response to oxygen-containing compound heart development animal organ development ventricular septum development cardiac septum development cardiac chamber development cardiac ventricle development response to 2,3,7,8-tetrachlorodibenzodioxine cellular response to 2,3,7,8-tetrachlorodibenzodioxine cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor response to cAMP cellular response to cAMP response to granulocyte macrophage colony-stimulating factor cellular response to granulocyte macrophage colony-stimulating factor stimulus negative regulation of intracellular signal transduction negative regulation of cAMP/PKA signal transduction intracellular signal transduction cAMP/PKA signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of cAMP/PKA signal transduction heart valve development response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus epithelium development endothelial cell differentiation endothelium development tissue development epithelial cell differentiation endothelial cell development epithelial cell development establishment of endothelial barrier adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery presynapse synapse cell junction membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery presynapse synapse cell junction membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system perinuclear region of cytoplasm mitochondrial membrane mitochondrion organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane organelle inner membrane mitochondrial inner membrane membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site
A, B	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A, B	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR003018	GAF domain	Domain
A, B	IPR003607	HD/PDEase domain	Domain
A, B	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain
A, B	IPR023088	3'5'-cyclic nucleotide phosphodiesterase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O00408	breast carcinoma breast cancer rheumatoid arthritis oligodendroglioma Pick disease Prevention of Cerebral Thrombosis tuberculosis astrocytic tumor invasive ductal breast carcinoma malignant ependymoma osteosarcoma pilocytic astrocytoma primitive neuroectodermal tumor atrial fibrillation ductal breast carcinoma in situ breast carcinoma breast cancer rheumatoid arthritis oligodendroglioma Pick disease Prevention of Cerebral Thrombosis tuberculosis astrocytic tumor invasive ductal breast carcinoma malignant ependymoma osteosarcoma pilocytic astrocytoma primitive neuroectodermal tumor atrial fibrillation ductal breast carcinoma in situ large cell medulloblastoma malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor breast fibroadenoma glioblastoma lung adenocarcinoma medulloblastoma

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.