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B0G0Y8

- PDE3_DICDI

UniProt

B0G0Y8 - PDE3_DICDI

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Protein

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

Gene
pde3, DDB_G0268634
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - 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

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)
  3. KM=145 µM for cAMP (catalytic domain expressed in E. Coli)
  4. 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

Sites

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

Enzyme and pathway databases

ReactomeiREACT_227374. cGMP effects.

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: Chromosome 1, UP000002195: 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.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni189 – 447259Catalytic By 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.
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

MAPQQNIMKQ LQQMQSSPYP SSSPSSTTVS QNNDNLNHNV HSLNNSSNNN    50
NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNSINEKNK INDNNNRGNS 100
DDGNNNNSNN NSNNNNSNNN NRDDEEEEGD DEDNNNNNNS NNNKIRGYND 150
NNDINDIFSI NFSSWSKSKD NLIENGVLIF EESGLYKELN LSKSSILNFL 200
SIVASSYRNN PFHSFNHAIA VTQTIFLILL KTNLFNILSP IEKLSIIIAS 250
ICHDLDHPAL SNRFQINMKS SIAVLYNNKS VLENHHLSIC LGILESKIGN 300
ELLSTLTVEE KKQFFRRVKI LILATDMENH FTYKKQFDDI ISTFSWDNSE 350
HRDLLLIMFL KSADISNELR SFDISNKWAN ALMEEFFNQS DLEKLNNLPL 400
TPFMEREKVV LHLTQVSFIE KFLLPSYQSL QNLLPSLEDF VQRIIENKEI 450
WSNNGSSSST TSSSPN 466
Length:466
Mass (Da):53,121
Last modified:March 18, 2008 - v1
Checksum:i1C3C557EC4D4089D
GO

Sequence cautioni

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

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
AY162269 Genomic DNA. Translation: AAN78319.1 . Sequence problems.
AAFI02000004 Genomic DNA. Translation: EDR41121.1 .
RefSeqi XP_001732951.1. XM_001732899.1.

3D structure databases

ProteinModelPortali B0G0Y8.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDBDRAFT_0190048.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0233681 ; DDB0233681 ; DDB_G0268634 .
GeneIDi 8616668.
KEGGi ddi:DDB_G0268634.

Organism-specific databases

dictyBasei DDB_G0268634. pde3.

Phylogenomic databases

eggNOGi NOG268427.
OMAi FFMLCEL.
PhylomeDBi B0G0Y8.

Enzyme and pathway databases

Reactomei REACT_227374. cGMP effects.

Family and domain databases

Gene3Di 1.10.1300.10. 1 hit.
InterProi IPR003607. HD/PDEase_dom.
IPR023088. PDEase.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view ]
Pfami PF00233. PDEase_I. 1 hit.
[Graphical view ]
PRINTSi PR00387. PDIESTERASE1.
SMARTi SM00471. HDc. 1 hit.
[Graphical view ]
PROSITEi PS00126. PDEASE_I. 1 hit.
[Graphical view ]
ProtoNeti Search...

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(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.
    , 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.

Entry informationi

Entry nameiPDE3_DICDI
AccessioniPrimary (citable) accession number: B0G0Y8
Secondary accession number(s): Q8I6Y6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: March 18, 2008
Last modified: September 3, 2014
This is version 35 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

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