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Protein

cGMP-specific 3',5'-cGMP phosphodiesterase 3

Gene

pde3

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Phosphodiesterase specific for cGMP, which is not activated by cGMP. Involved in the degradation of intracellular cGMP.2 Publications

Catalytic activityi

Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.

Cofactori

a divalent metal cationBy similarityNote: 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 regulationi

Inhibited by 3-isobutyl-1-methylxanthine (IBMX).

Kineticsi

cAMP/cGMP selectivity of 0.0015.

  1. KM=0.22 µM for cGMP (catalytic domain expressed in E. Coli)2 Publications
  2. KM=0.33 µM for cGMP (catalytic domain expressed in Dictyostelium)2 Publications
  3. KM=145 µM for cAMP (catalytic domain expressed in E. Coli)2 Publications
  4. KM=207 µM for cAMP (catalytic domain expressed in Dictyostelium)2 Publications

Vmax=150 pmol/min/mg enzyme with cAMP as substrate2 Publications

Vmax=2 pmol/min/mg enzyme with cGMP as substrate2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei213 – 2131Proton donorBy similarity
Metal bindingi217 – 2171Divalent metal cation 1By similarity
Metal bindingi253 – 2531Divalent metal cation 1By similarity
Metal bindingi254 – 2541Divalent metal cation 1By similarity
Metal bindingi254 – 2541Divalent metal cation 2By similarity
Metal bindingi364 – 3641Divalent metal cation 1By similarity

GO - Molecular functioni

  1. 3',5'-cyclic-GMP phosphodiesterase activity Source: dictyBase
  2. cGMP binding Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cGMP catabolic process Source: dictyBase
  2. signal transduction Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

cGMP, cGMP-binding, Manganese, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
cGMP-specific 3',5'-cGMP phosphodiesterase 3 (EC:3.1.4.35)
Alternative name(s):
Phosphodiesterase 3
Short name:
DdPDE3
Gene namesi
Name:pde3
ORF Names:DDB_G0268634
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195 Componentsi: Chromosome 1, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0268634. pde3.

Subcellular locationi

Cytoplasmcytosol 2 Publications

GO - Cellular componenti

  1. cytosol Source: UniProtKB-SubCell
  2. intracellular Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Shows a moderate phenotype with increased basal cGMP levels, but only a small effect on cAMP-stimulated cGMP levels.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 466466cGMP-specific 3',5'-cGMP phosphodiesterase 3PRO_0000363969Add
BLAST

Expressioni

Developmental stagei

Expression is constant throughout the development.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi44689.DDBDRAFT_0190048.

Structurei

3D structure databases

ProteinModelPortaliB0G0Y8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni189 – 447259CatalyticBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi48 – 8336Poly-AsnAdd
BLAST
Compositional biasi104 – 12118Poly-AsnAdd
BLAST
Compositional biasi125 – 1284Poly-Glu
Compositional biasi134 – 14310Poly-Asn
Compositional biasi456 – 4594Poly-Ser

Domaini

Composed of a C-terminal catalytic domain containing two putative divalent metal sites and an N-terminal regulatory domain.

Sequence similaritiesi

Phylogenomic databases

eggNOGiNOG268427.
InParanoidiB0G0Y8.
OMAiFFMLCEL.
PhylomeDBiB0G0Y8.

Family and domain databases

Gene3Di1.10.1300.10. 1 hit.
InterProiIPR003607. HD/PDEase_dom.
IPR023088. PDEase.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view]
PfamiPF00233. PDEase_I. 1 hit.
[Graphical view]
PRINTSiPR00387. PDIESTERASE1.
SMARTiSM00471. HDc. 1 hit.
[Graphical view]
PROSITEiPS00126. PDEASE_I. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B0G0Y8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPQQNIMKQ LQQMQSSPYP SSSPSSTTVS QNNDNLNHNV HSLNNSSNNN
60 70 80 90 100
NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNSINEKNK INDNNNRGNS
110 120 130 140 150
DDGNNNNSNN NSNNNNSNNN NRDDEEEEGD DEDNNNNNNS NNNKIRGYND
160 170 180 190 200
NNDINDIFSI NFSSWSKSKD NLIENGVLIF EESGLYKELN LSKSSILNFL
210 220 230 240 250
SIVASSYRNN PFHSFNHAIA VTQTIFLILL KTNLFNILSP IEKLSIIIAS
260 270 280 290 300
ICHDLDHPAL SNRFQINMKS SIAVLYNNKS VLENHHLSIC LGILESKIGN
310 320 330 340 350
ELLSTLTVEE KKQFFRRVKI LILATDMENH FTYKKQFDDI ISTFSWDNSE
360 370 380 390 400
HRDLLLIMFL KSADISNELR SFDISNKWAN ALMEEFFNQS DLEKLNNLPL
410 420 430 440 450
TPFMEREKVV LHLTQVSFIE KFLLPSYQSL QNLLPSLEDF VQRIIENKEI
460
WSNNGSSSST TSSSPN
Length:466
Mass (Da):53,121
Last modified:March 17, 2008 - v1
Checksum:i1C3C557EC4D4089D
GO

Sequence cautioni

The sequence AAN78319.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY162269 Genomic DNA. Translation: AAN78319.1. Sequence problems.
AAFI02000004 Genomic DNA. Translation: EDR41121.1.
RefSeqiXP_001732951.1. XM_001732899.1.

Genome annotation databases

EnsemblProtistsiDDB0233681; DDB0233681; DDB_G0268634.
GeneIDi8616668.
KEGGiddi:DDB_G0268634.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY162269 Genomic DNA. Translation: AAN78319.1. Sequence problems.
AAFI02000004 Genomic DNA. Translation: EDR41121.1.
RefSeqiXP_001732951.1. XM_001732899.1.

3D structure databases

ProteinModelPortaliB0G0Y8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDBDRAFT_0190048.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0233681; DDB0233681; DDB_G0268634.
GeneIDi8616668.
KEGGiddi:DDB_G0268634.

Organism-specific databases

dictyBaseiDDB_G0268634. pde3.

Phylogenomic databases

eggNOGiNOG268427.
InParanoidiB0G0Y8.
OMAiFFMLCEL.
PhylomeDBiB0G0Y8.

Family and domain databases

Gene3Di1.10.1300.10. 1 hit.
InterProiIPR003607. HD/PDEase_dom.
IPR023088. PDEase.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view]
PfamiPF00233. PDEase_I. 1 hit.
[Graphical view]
PRINTSiPR00387. PDIESTERASE1.
SMARTiSM00471. HDc. 1 hit.
[Graphical view]
PROSITEiPS00126. PDEASE_I. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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(2000) [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.
    , 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(2004) [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(2001) [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(2004) [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(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.

Entry informationi

Entry nameiPDE3_DICDI
AccessioniPrimary (citable) accession number: B0G0Y8
Secondary accession number(s): Q8I6Y6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 9, 2009
Last sequence update: March 17, 2008
Last modified: January 6, 2015
This is version 39 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.