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B0G0Y8

- PDE3_DICDI

UniProt

B0G0Y8 - PDE3_DICDI

Protein

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

Gene

pde3

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 36 (01 Oct 2014)
      Sequence version 1 (18 Mar 2008)
      Previous versions | rss
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    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.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

    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

    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.
    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

    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: October 1, 2014
    This is version 36 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