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Title :   REGULATORY SEGMENT OF MOUSE 3',5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 2A, CONTAINING THE GAF A AND GAF B DOMAINS

Authors :   S. Martinez, A. Wu, N. Glavas, X. Tang, S. Turley, W. Hol, J. Beavo

Date :   04 Aug 02 (Deposition) - 02 Oct 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.86

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: A  (4x)

Keywords :   Gaf Domain, 3', 5'-Cyclic Nucleotide Phosphodiesterase, 3', 5'- Guanosine Monophosphate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. E. Martinez, A. Y. Wu, N. A. Glavas, X. B. Tang, S. Turley, W. G. Hol, J. A. Beavo
The Two Gaf Domains In Phosphodiesterase 2A Have Distinct Roles In Dimerization And In Cgmp Binding.
Proc. Natl. Acad. Sci. Usa V. 99 13260 2002
PubMed-ID: 12271124 | Reference-DOI: 10.1073/PNAS.192374899

Molecule 1 - 3',5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 2A
	Chains	:	A
	EC Number	:	3.1.4.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PRUNH
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	REGULATORY DOMAIN (RESIDUES 207-566)
	Gene	:	PDE2A
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:	A
Biological Unit 3 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PCG	1	Ligand/Ion	CYCLIC GUANOSINE MONOPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PCG	1	Ligand/Ion	CYCLIC GUANOSINE MONOPHOSPHATE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	PCG	-1	Ligand/Ion	CYCLIC GUANOSINE MONOPHOSPHATE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	PCG	4	Ligand/Ion	CYCLIC GUANOSINE MONOPHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1 , HOH A:2 , HOH A:3 , ILE A:422 , CYS A:423 , SER A:424 , PHE A:438 , ASP A:439 , GLY A:457 , ILE A:458 , ALA A:459 , PHE A:480 , TYR A:481 , VAL A:484 , ASP A:485 , PHE A:490 , THR A:492 , ILE A:495 , GLU A:512	BINDING SITE FOR RESIDUE PCG A 160

Asymmetric Unit

No.	Residues
1	A:386	-	A:386

(no "Cis Peptide Bond" information available for 1MC0)

(no "SAP(SNP)/Variant" information available for 1MC0)

(no "PROSITE Motif" information available for 1MC0)

(no "Exon" information available for 1MC0)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:341
 aligned with PDE2A_MOUSE | Q922S4 from UniProtKB/Swiss-Prot  Length:916

    Alignment length:341
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537 
          PDE2A_MOUSE   198 YTDHDRKILQLCGELFDLDATSLQLKVLQYLQQETQATHCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTMGRLGQVVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLCVPVISRATDQVVALACAFNKLGGDFFTDEDEHVIQHCFHYTGTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQY 538
               SCOP domains d1mc0a1 A:215-401 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains                                                                                                    d1mc0a2 A:402-555 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains                                                                    SCOP domains
               CATH domains 1mc0A01 A:215-372  [code=3.30.450.40, no name defined]                                                                                                        ---------------------------1mc0A02 A:400-555  [code=3.30.450.40, no name defined]                                                                                                       CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAF-1mc0A01 A:402-541                                                                                                                       -------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAF-1mc0A02 A:402-541                                                                                                                       -------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeee..eeeeeeeeee....hhhhhhhhh..ee.hhhhhhhhhhhhhhhh.....eeeeeee......eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhheeeeeeeee....eeeeee..ee........ee...hhhhhhhhhhh..eee............hhhhhh.....eeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mc0 A 215 YTDHDRKILQLCGELFDLDATSLQLKVLQYLQQETQATHCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTMGRLGQVVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLCVPVISRATDQVVALACAFNKLGGDFFTDEDEHVIQHCFHYTGTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQY 555
                                   224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Profilin-like (304)

Superfamily: GAF domain-like (54)

Family: GAF domain (24)

Protein domain: 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains (1)

Mouse (Mus musculus) [TaxId: 10090] (1)

1a	d1mc0a1	A:215-401
1b	d1mc0a2	A:402-555

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta-Lactamase (202)

Homologous Superfamily: [code=3.30.450.40, no name defined] (27)

House mouse (Mus musculus) (1)

1a	1mc0A02	A:400-555
1b	1mc0A01	A:215-372

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: GAF (30)

Mus musculus (Mouse) (2)

1a	GAF-1mc0A01	A:402-541
1b	GAF-1mc0A02	A:402-541

Asymmetric Unit(hide GO term definitions)

Chain A (PDE2A_MOUSE | Q922S4)

molecular function
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0036004	GAF domain binding	Interacting selectively and non-covalently with the GAF domain of a protein.
	GO:0030911	TPR domain binding	Interacting selectively and non-covalently with a tetratricopeptide repeat (TPR) domain of a protein, the consensus sequence of which is defined by a pattern of small and large hydrophobic amino acids and a structure composed of helices.
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0030553	cGMP binding	Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
	GO:0004118	cGMP-stimulated cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is increased in the presence of cGMP.
	GO:0004112	cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0035904	aorta development	The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
	GO:0006198	cAMP catabolic process	The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0019933	cAMP-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
	GO:0046069	cGMP catabolic process	The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
	GO:0019934	cGMP-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via cyclic GMP (cGMP). Includes production of cGMP, and downstream effectors that further transmit the signal within the cell.
	GO:0003279	cardiac septum development	The progression of a cardiac septum over time, from its initial formation to the mature structure.
	GO:0071321	cellular response to cGMP	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cGMP (cyclic GMP, guanosine 3',5'-cyclophosphate) stimulus.
	GO:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0097011	cellular response to granulocyte macrophage colony-stimulating factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a granulocyte macrophage colony-stimulating factor stimulus.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0036006	cellular response to macrophage colony-stimulating factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a macrophage colony-stimulating factor stimulus.
	GO:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0060976	coronary vasculature development	The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
	GO:0061028	establishment of endothelial barrier	The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0003170	heart valve development	The progression of a heart valve over time, from its formation to the mature structure. A heart valve is a structure that restricts the flow of blood to different regions of the heart and forms from an endocardial cushion.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0030818	negative regulation of cAMP biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0033159	negative regulation of protein import into nucleus, translocation	Any process that stops, prevents or reduces the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0043116	negative regulation of vascular permeability	Any process that reduces the extent to which blood vessels can be pervaded by fluid.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:0043117	positive regulation of vascular permeability	Any process that increases the extent to which blood vessels can be pervaded by fluid.
	GO:0006626	protein targeting to mitochondrion	The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
	GO:0030823	regulation of cGMP metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0003281	ventricular septum development	The progression of the ventricular septum over time from its formation to the mature structure.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0042734	presynaptic membrane	A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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