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B0G0Y8 (PDE3_DICDI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 34. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismDictyostelium discoideum (Slime mold) [Reference proteome]
Taxonomic identifier44689 [NCBI]
Taxonomic lineageEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium

Protein attributes

Sequence length466 AA.
Sequence statusComplete.
Protein existenceEvidence 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

Cytoplasmcytosol 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) Ref.1 Ref.3

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 466466cGMP-specific 3',5'-cGMP phosphodiesterase 3
PRO_0000363969

Regions

Region189 – 447259Catalytic By similarity
Compositional bias48 – 8336Poly-Asn
Compositional bias104 – 12118Poly-Asn
Compositional bias125 – 1284Poly-Glu
Compositional bias134 – 14310Poly-Asn
Compositional bias456 – 4594Poly-Ser

Sites

Active site2131Proton donor By similarity
Metal binding2171Divalent metal cation 1 By similarity
Metal binding2531Divalent metal cation 1 By similarity
Metal binding2541Divalent metal cation 1 By similarity
Metal binding2541Divalent metal cation 2 By similarity
Metal binding3641Divalent metal cation 1 By similarity

Sequences

Sequence LengthMass (Da)Tools
B0G0Y8 [UniParc].

Last modified March 18, 2008. Version 1.
Checksum: 1C3C557EC4D4089D

FASTA46653,121
        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 

« Hide

References

« Hide '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] [Europe PMC] [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. expand/collapse author list , 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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.
RefSeqXP_001732951.1. XM_001732899.1.

3D structure databases

ProteinModelPortalB0G0Y8.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING44689.DDBDRAFT_0190048.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsDDB0233681; DDB0233681; DDB_G0268634.
GeneID8616668.
KEGGddi:DDB_G0268634.

Organism-specific databases

dictyBaseDDB_G0268634. pde3.

Phylogenomic databases

eggNOGNOG268427.
OMAFFMLCEL.
PhylomeDBB0G0Y8.

Family and domain databases

Gene3D1.10.1300.10. 1 hit.
InterProIPR003607. HD/PDEase_dom.
IPR023088. PDEase.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view]
PfamPF00233. PDEase_I. 1 hit.
[Graphical view]
PRINTSPR00387. PDIESTERASE1.
SMARTSM00471. HDc. 1 hit.
[Graphical view]
PROSITEPS00126. PDEASE_I. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePDE3_DICDI
AccessionPrimary (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: May 14, 2014
This is version 34 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)

Relevant documents

SIMILARITY comments

Index of protein domains and families

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase