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Protein

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

Gene

pde3

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: -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
  1. Vmax=150 pmol/min/mg enzyme with cAMP as substrate2 Publications
  2. Vmax=2 pmol/min/mg enzyme with cGMP as substrate2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei213Proton donorBy similarity1
Metal bindingi217Divalent metal cation 1By similarity1
Metal bindingi253Divalent metal cation 1By similarity1
Metal bindingi254Divalent metal cation 1By similarity1
Metal bindingi254Divalent metal cation 2By similarity1
Metal bindingi364Divalent metal cation 1By similarity1

GO - Molecular functioni

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

GO - Biological processi

  • cGMP catabolic process Source: dictyBase
  • signal transduction Source: InterPro

Keywordsi

Molecular functionHydrolase
LigandcGMP, cGMP-binding, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-DDI-418457 cGMP effects
SABIO-RKiB0G0Y8

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 lineageiEukaryotaAmoebozoaMycetozoaDictyostelidsDictyostelialesDictyosteliaceaeDictyostelium
Proteomesi
  • UP000002195 Componentsi: Chromosome 1, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0268634 pde3

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB-SubCell
  • 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)DescriptionActionsGraphical viewLength
ChainiPRO_00003639691 – 466cGMP-specific 3',5'-cGMP phosphodiesterase 3Add BLAST466

Proteomic databases

PaxDbiB0G0Y8

Expressioni

Developmental stagei

Expression is constant throughout the development.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi44689.DDB0233681

Structurei

3D structure databases

ProteinModelPortaliB0G0Y8
SMRiB0G0Y8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini137 – 458PDEasePROSITE-ProRule annotationAdd BLAST322

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi48 – 83Poly-AsnAdd BLAST36
Compositional biasi104 – 121Poly-AsnAdd BLAST18
Compositional biasi125 – 128Poly-Glu4
Compositional biasi134 – 143Poly-Asn10
Compositional biasi456 – 459Poly-Ser4

Domaini

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG3689 Eukaryota
ENOG410XRI7 LUCA
InParanoidiB0G0Y8
OMAiWANALME
PhylomeDBiB0G0Y8

Family and domain databases

CDDicd00077 HDc, 1 hit
Gene3Di1.10.1300.10, 1 hit
InterProiView protein in InterPro
IPR003607 HD/PDEase_dom
IPR023088 PDEase
IPR002073 PDEase_catalytic_dom
IPR036971 PDEase_catalytic_dom_sf
IPR023174 PDEase_CS
PfamiView protein in Pfam
PF00233 PDEase_I, 1 hit
PRINTSiPR00387 PDIESTERASE1
SMARTiView protein in SMART
SM00471 HDc, 1 hit
PROSITEiView protein in PROSITE
PS00126 PDEASE_I_1, 1 hit
PS51845 PDEASE_I_2, 1 hit

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 18, 2008 - v1
Checksum:i1C3C557EC4D4089D
GO

Sequence cautioni

The sequence AAN78319 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

EnsemblProtistsiEDR41121; EDR41121; DDB_G0268634
GeneIDi8616668
KEGGiddi:DDB_G0268634

Similar proteinsi

Entry informationi

Entry nameiPDE3_DICDI
AccessioniPrimary (citable) accession number: B0G0Y8
Secondary accession number(s): Q8I6Y6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: March 18, 2008
Last modified: March 28, 2018
This is version 54 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health