Reviewed, UniProtKB/Swiss-Prot B0G0Y8 (PDE3_DICDI)

Names and origin

Protein names

Recommended name:
    cGMP-specific 3',5'-cGMP phosphodiesterase 3
    EC=3.1.4.35
Alternative name(s):
    Phosphodiesterase 3
      Short name=DdPDE3

Gene names

Name:	pde3
ORF Names:	DDB_G0268634

Organism

Dictyostelium discoideum (Slime mold) [Complete proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	466 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Phosphodiesterase specific for cGMP, which is not activated by cGMP. Involved in the degradation of intracellular cGMP. Ref.1 Ref.3
Catalytic activity	Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
Cofactor	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 By similarity.
Enzyme regulation	Inhibited by 3-isobutyl-1-methylxanthine (IBMX).
Subcellular location	Cytoplasm › cytosol Ref.3 Ref.5.
Developmental stage	Expression is constant throughout the development. Ref.1
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. Ref.1
Sequence similarities	Belongs to the cyclic nucleotide phosphodiesterase family.
Biophysicochemical properties	Kinetic parameters: cAMP/cGMP selectivity of 0.0015. KM=0.22 µM for cGMP (catalytic domain expressed in E. Coli) KM=0.33 µM for cGMP (catalytic domain expressed in Dictyostelium) KM=145 µM for cAMP (catalytic domain expressed in E. Coli) KM=207 µM for cAMP (catalytic domain expressed in Dictyostelium) Vmax=150 pmol/min/mg enzyme with cAMP as substrate Vmax=2 pmol/min/mg enzyme with cGMP as substrate
Sequence caution	The sequence AAN78319.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Manganese Metal-binding Nucleotide-binding cGMP cGMP-binding
Molecular function	Hydrolase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	cGMP catabolic process Traceable author statement. Source: dictyBase signal transduction Inferred from electronic annotation. Source: InterPro
Cellular component	cytosol Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	3',5'-cyclic-GMP phosphodiesterase activity Traceable author statement. Source: dictyBase cGMP binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 466	466	cGMP-specific 3',5'-cGMP phosphodiesterase 3		PRO_0000363969
Regions
	Region	189 – 447	259	Catalytic By similarity
	Compositional bias	48 – 83	36	Poly-Asn
	Compositional bias	104 – 121	18	Poly-Asn
	Compositional bias	125 – 128	4	Poly-Glu
	Compositional bias	134 – 143	10	Poly-Asn
	Compositional bias	456 – 459	4	Poly-Ser
Sites
	Active site	213	1	Proton donor By similarity
	Metal binding	217	1	Divalent metal cation 1 By similarity
	Metal binding	253	1	Divalent metal cation 1 By similarity
	Metal binding	254	1	Divalent metal cation 1 By similarity
	Metal binding	254	1	Divalent metal cation 2 By similarity
	Metal binding	364	1	Divalent metal cation 1 By similarity

Sequences

	Sequence		Length	Mass (Da)
	B0G0Y8-1 [UniParc]. Last modified March 18, 2008. Version 1. Checksum: 1C3C557EC4D4089D	FASTA	466	53,121
	10 20 30 40 50 60 MAPQQNIMKQ LQQMQSSPYP SSSPSSTTVS QNNDNLNHNV HSLNNSSNNN NNNNNNNNNN 70 80 90 100 110 120 NNNNNNNNNN NNNNNNNNNN NNNSINEKNK INDNNNRGNS DDGNNNNSNN NSNNNNSNNN 130 140 150 160 170 180 NRDDEEEEGD DEDNNNNNNS NNNKIRGYND NNDINDIFSI NFSSWSKSKD NLIENGVLIF 190 200 210 220 230 240 EESGLYKELN LSKSSILNFL SIVASSYRNN PFHSFNHAIA VTQTIFLILL KTNLFNILSP 250 260 270 280 290 300 IEKLSIIIAS ICHDLDHPAL SNRFQINMKS SIAVLYNNKS VLENHHLSIC LGILESKIGN 310 320 330 340 350 360 ELLSTLTVEE KKQFFRRVKI LILATDMENH FTYKKQFDDI ISTFSWDNSE HRDLLLIMFL 370 380 390 400 410 420 KSADISNELR SFDISNKWAN ALMEEFFNQS DLEKLNNLPL TPFMEREKVV LHLTQVSFIE 430 440 450 460 KFLLPSYQSL QNLLPSLEDF VQRIIENKEI WSNNGSSSST TSSSPN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and characterization of DdPDE3, a cGMP-selective phosphodiesterase from Dictyostelium." Kuwayama H., Snippe H., Derks M., Roelofs J., Van Haastert P.J.M. Biochem. J. 353:635-644(2001) [PubMed: 11171061] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, CHARACTERIZATION, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
[2]	"The genome of the social amoeba Dictyostelium discoideum." 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. Nature 435:43-57(2005) [PubMed: 15875012] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.
[3]	"Identification and characterization of two unusual cGMP-stimulated phoshodiesterases in dictyostelium." Bosgraaf L., Russcher H., Snippe H., Bader S., Wind J., Van Haastert P.J.M. Mol. Biol. Cell 13:3878-3889(2002) [PubMed: 12429832] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES.
[4]	"Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes." Booth E.O., Van Driessche N., Zhuchenko O., Kuspa A., Shaulsky G. Bioinformatics 21:4371-4377(2005) [PubMed: 16234315] [Abstract] Cited for: IDENTIFICATION.
[5]	"Seven Dictyostelium discoideum phosphodiesterases degrade three pools of cAMP and cGMP." Bader S., Kortholt A., Van Haastert P.J.M. Biochem. J. 402:153-161(2007) [PubMed: 17040207] [Abstract] Cited for: SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY162269 Genomic DNA. Translation: AAN78319.1. Sequence problems. AAFI02000004 Genomic DNA. Translation: EDR41121.1.
RefSeq	XP_001732951.1.
3D structure databases
SMR	B0G0Y8. Positions 151-453.
ModBase	Search...
Genome annotation databases
GeneID	8616668.
KEGG	ddi:DDB_0233681.
Organism-specific databases
dictyBase	DDB_G0268634. pde3.
Phylogenomic databases
eggNOG	KOG3689.
HOGENOM	HBG406754.
Family and domain databases
InterPro	IPR003607. Metal-dep_PHydrolase_HD_dom. IPR002073. PDEase. [Graphical view]
Pfam	PF00233. PDEase_I. 1 hit. [Graphical view]
PRINTS	PR00387. PDIESTERASE1.
SMART	SM00471. HDc. 1 hit. [Graphical view]
PROSITE	PS00126. PDEASE_I. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PDE3_DICDI

Accession

Primary (citable) accession number: B0G0Y8
Secondary accession number(s): Q8I6Y6

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 10, 2009
Last sequence update:	March 18, 2008
Last modified:	February 9, 2010
This is version 15 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)