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cGMP-specific 3',5'-cGMP phosphodiesterase 3 (EC 3.1.4.35) (Phosphodiesterase 3) (DdPDE3)

 PDE3_DICDI              Reviewed;         466 AA.
B0G0Y8; Q8I6Y6;
10-FEB-2009, integrated into UniProtKB/Swiss-Prot.
18-MAR-2008, sequence version 1.
25-OCT-2017, entry version 50.
RecName: Full=cGMP-specific 3',5'-cGMP phosphodiesterase 3;
EC=3.1.4.35;
AltName: Full=Phosphodiesterase 3;
Short=DdPDE3;
Name=pde3; ORFNames=DDB_G0268634;
Dictyostelium discoideum (Slime mold).
Eukaryota; Amoebozoa; Mycetozoa; Dictyosteliida; Dictyostelium.
NCBI_TaxID=44689;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, BIOPHYSICOCHEMICAL
PROPERTIES, CHARACTERIZATION, DEVELOPMENTAL STAGE, AND DISRUPTION
PHENOTYPE.
PubMed=11171061; DOI=10.1042/0264-6021:3530635;
Kuwayama H., Snippe H., Derks M., Roelofs J., Van Haastert P.J.M.;
"Identification and characterization of DdPDE3, a cGMP-selective
phosphodiesterase from Dictyostelium.";
Biochem. J. 353:635-644(2001).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=AX4;
PubMed=15875012; DOI=10.1038/nature03481;
Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A.,
Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q.,
Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F.,
Bankier A.T., Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P.,
Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P.,
Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N.,
Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M.,
Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I.,
Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R.,
Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
Knights A., Loulseged H., Mungall K.L., Oliver K., Price C.,
Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D.,
Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S.,
Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T.,
Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A.,
Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M.,
Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G.,
Kuspa A.;
"The genome of the social amoeba Dictyostelium discoideum.";
Nature 435:43-57(2005).
[3]
FUNCTION, SUBCELLULAR LOCATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=12429832; DOI=10.1091/mbc.E02-05-0302;
Bosgraaf L., Russcher H., Snippe H., Bader S., Wind J.,
Van Haastert P.J.M.;
"Identification and characterization of two unusual cGMP-stimulated
phoshodiesterases in dictyostelium.";
Mol. Biol. Cell 13:3878-3889(2002).
[4]
IDENTIFICATION.
PubMed=16234315; DOI=10.1093/bioinformatics/bti726;
Booth E.O., Van Driessche N., Zhuchenko O., Kuspa A., Shaulsky G.;
"Microarray phenotyping in Dictyostelium reveals a regulon of
chemotaxis genes.";
Bioinformatics 21:4371-4377(2005).
[5]
SUBCELLULAR LOCATION.
PubMed=17040207; DOI=10.1042/BJ20061153;
Bader S., Kortholt A., Van Haastert P.J.M.;
"Seven Dictyostelium discoideum phosphodiesterases degrade three pools
of cAMP and cGMP.";
Biochem. J. 402:153-161(2007).
-!- FUNCTION: Phosphodiesterase specific for cGMP, which is not
activated by cGMP. Involved in the degradation of intracellular
cGMP. {ECO:0000269|PubMed:11171061, ECO:0000269|PubMed:12429832}.
-!- CATALYTIC ACTIVITY: Guanosine 3',5'-cyclic phosphate + H(2)O =
guanosine 5'-phosphate.
-!- COFACTOR:
Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
Evidence={ECO:0000250};
Note=Binds 2 divalent metal cations per subunit. Site 1 may
preferentially bind zinc ions, while site 2 has a preference for
magnesium and/or manganese ions. {ECO:0000250};
-!- ENZYME REGULATION: Inhibited by 3-isobutyl-1-methylxanthine
(IBMX).
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.22 uM for cGMP (catalytic domain expressed in E. Coli)
{ECO:0000269|PubMed:11171061, ECO:0000269|PubMed:12429832};
KM=0.33 uM for cGMP (catalytic domain expressed in
Dictyostelium) {ECO:0000269|PubMed:11171061,
ECO:0000269|PubMed:12429832};
KM=145 uM for cAMP (catalytic domain expressed in E. Coli)
{ECO:0000269|PubMed:11171061, ECO:0000269|PubMed:12429832};
KM=207 uM for cAMP (catalytic domain expressed in Dictyostelium)
{ECO:0000269|PubMed:11171061, ECO:0000269|PubMed:12429832};
Vmax=150 pmol/min/mg enzyme with cAMP as substrate
{ECO:0000269|PubMed:11171061, ECO:0000269|PubMed:12429832};
Vmax=2 pmol/min/mg enzyme with cGMP as substrate
{ECO:0000269|PubMed:11171061, ECO:0000269|PubMed:12429832};
Note=cAMP/cGMP selectivity of 0.0015.;
-!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
{ECO:0000269|PubMed:12429832, ECO:0000269|PubMed:17040207}.
-!- DEVELOPMENTAL STAGE: Expression is constant throughout the
development. {ECO:0000269|PubMed:11171061}.
-!- DOMAIN: Composed of a C-terminal catalytic domain containing two
putative divalent metal sites and an N-terminal regulatory domain.
-!- DISRUPTION PHENOTYPE: Shows a moderate phenotype with increased
basal cGMP levels, but only a small effect on cAMP-stimulated cGMP
levels. {ECO:0000269|PubMed:11171061}.
-!- SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase
family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAN78319.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AY162269; AAN78319.1; ALT_SEQ; Genomic_DNA.
EMBL; AAFI02000004; EDR41121.1; -; Genomic_DNA.
RefSeq; XP_001732951.1; XM_001732899.1.
ProteinModelPortal; B0G0Y8; -.
SMR; B0G0Y8; -.
STRING; 44689.DDB0233681; -.
PaxDb; B0G0Y8; -.
EnsemblProtists; EDR41121; EDR41121; DDB_G0268634.
GeneID; 8616668; -.
KEGG; ddi:DDB_G0268634; -.
dictyBase; DDB_G0268634; pde3.
eggNOG; KOG3689; Eukaryota.
eggNOG; ENOG410XRI7; LUCA.
InParanoid; B0G0Y8; -.
OMA; WANALME; -.
PhylomeDB; B0G0Y8; -.
Reactome; R-DDI-418457; cGMP effects.
PRO; PR:B0G0Y8; -.
Proteomes; UP000002195; Chromosome 1.
Proteomes; UP000002195; Unassembled WGS sequence.
GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
GO; GO:0005622; C:intracellular; TAS:dictyBase.
GO; GO:0047555; F:3',5'-cyclic-GMP phosphodiesterase activity; TAS:dictyBase.
GO; GO:0030553; F:cGMP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0046069; P:cGMP catabolic process; TAS:dictyBase.
GO; GO:0007165; P:signal transduction; IEA:InterPro.
CDD; cd00077; HDc; 1.
Gene3D; 1.10.1300.10; -; 1.
InterPro; IPR003607; HD/PDEase_dom.
InterPro; IPR023088; PDEase.
InterPro; IPR002073; PDEase_catalytic_dom.
InterPro; IPR036971; PDEase_catalytic_dom_sf.
InterPro; IPR023174; PDEase_CS.
Pfam; PF00233; PDEase_I; 1.
PRINTS; PR00387; PDIESTERASE1.
SMART; SM00471; HDc; 1.
PROSITE; PS00126; PDEASE_I; 1.
1: Evidence at protein level;
cGMP; cGMP-binding; Complete proteome; Cytoplasm; Hydrolase;
Manganese; Metal-binding; Nucleotide-binding; Reference proteome.
CHAIN 1 466 cGMP-specific 3',5'-cGMP
phosphodiesterase 3.
/FTId=PRO_0000363969.
REGION 189 447 Catalytic. {ECO:0000250}.
COMPBIAS 48 83 Poly-Asn.
COMPBIAS 104 121 Poly-Asn.
COMPBIAS 125 128 Poly-Glu.
COMPBIAS 134 143 Poly-Asn.
COMPBIAS 456 459 Poly-Ser.
ACT_SITE 213 213 Proton donor. {ECO:0000250}.
METAL 217 217 Divalent metal cation 1. {ECO:0000250}.
METAL 253 253 Divalent metal cation 1. {ECO:0000250}.
METAL 254 254 Divalent metal cation 1. {ECO:0000250}.
METAL 254 254 Divalent metal cation 2. {ECO:0000250}.
METAL 364 364 Divalent metal cation 1. {ECO:0000250}.
SEQUENCE 466 AA; 53121 MW; 1C3C557EC4D4089D CRC64;
MAPQQNIMKQ LQQMQSSPYP SSSPSSTTVS QNNDNLNHNV HSLNNSSNNN NNNNNNNNNN
NNNNNNNNNN NNNNNNNNNN NNNSINEKNK INDNNNRGNS DDGNNNNSNN NSNNNNSNNN
NRDDEEEEGD DEDNNNNNNS NNNKIRGYND NNDINDIFSI NFSSWSKSKD NLIENGVLIF
EESGLYKELN LSKSSILNFL SIVASSYRNN PFHSFNHAIA VTQTIFLILL KTNLFNILSP
IEKLSIIIAS ICHDLDHPAL SNRFQINMKS SIAVLYNNKS VLENHHLSIC LGILESKIGN
ELLSTLTVEE KKQFFRRVKI LILATDMENH FTYKKQFDDI ISTFSWDNSE HRDLLLIMFL
KSADISNELR SFDISNKWAN ALMEEFFNQS DLEKLNNLPL TPFMEREKVV LHLTQVSFIE
KFLLPSYQSL QNLLPSLEDF VQRIIENKEI WSNNGSSSST TSSSPN


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