PDE2_CAEEL
ID PDE2_CAEEL Reviewed; 831 AA.
AC P30645; Q65ZC7; Q7JMU8;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 4.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Probable 3',5'-cyclic phosphodiesterase pde-2;
DE EC=3.1.4.17;
GN Name=pde-2 {ECO:0000312|WormBase:R08D7.6a};
GN ORFNames=R08D7.6 {ECO:0000312|WormBase:R08D7.6a};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=7906398; DOI=10.1038/368032a0;
RA Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J.,
RA Burton J., Connell M., Copsey T., Cooper J., Coulson A., Craxton M.,
RA Dear S., Du Z., Durbin R., Favello A., Fraser A., Fulton L., Gardner A.,
RA Green P., Hawkins T., Hillier L., Jier M., Johnston L., Jones M.,
RA Kershaw J., Kirsten J., Laisster N., Latreille P., Lightning J., Lloyd C.,
RA Mortimore B., O'Callaghan M., Parsons J., Percy C., Rifken L., Roopra A.,
RA Saunders D., Shownkeen R., Sims M., Smaldon N., Smith A., Smith M.,
RA Sonnhammer E., Staden R., Sulston J., Thierry-Mieg J., Thomas K.,
RA Vaudin M., Vaughan K., Waterston R., Watson A., Weinstock L.,
RA Wilkinson-Sproat J., Wohldman P.;
RT "2.2 Mb of contiguous nucleotide sequence from chromosome III of C.
RT elegans.";
RL Nature 368:32-38(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND ALTERNATIVE SPLICING.
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [3]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=26434723; DOI=10.1534/genetics.115.177543;
RA Fujiwara M., Hino T., Miyamoto R., Inada H., Mori I., Koga M., Miyahara K.,
RA Ohshima Y., Ishihara T.;
RT "The importance of cGMP signaling in sensory cilia for body size regulation
RT in Caenorhabditis elegans.";
RL Genetics 201:1497-1510(2015).
CC -!- FUNCTION: May negatively regulate the activity of cGMP-dependent
CC protein kinase egl-4 which in turn controls body size.
CC {ECO:0000269|PubMed:26434723}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-
CC phosphate + H(+); Xref=Rhea:RHEA:14653, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57867, ChEBI:CHEBI:58464; EC=3.1.4.17;
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250};
CC Note=Binds 2 divalent metal cations per subunit. Site 1 may
CC preferentially bind zinc ions, while site 2 has a preference for
CC magnesium and/or manganese ions. {ECO:0000250};
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=a {ECO:0000312|WormBase:R08D7.6a};
CC IsoId=P30645-1; Sequence=Displayed;
CC Name=b {ECO:0000312|WormBase:R08D7.6b};
CC IsoId=P30645-3; Sequence=VSP_014355;
CC -!- DISRUPTION PHENOTYPE: Reduced body size and an egg-laying constitutive
CC phenotype. {ECO:0000269|PubMed:26434723}.
CC -!- SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase family.
CC {ECO:0000305}.
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DR EMBL; Z12017; CAA78052.3; -; Genomic_DNA.
DR EMBL; Z12017; CAE47469.2; -; Genomic_DNA.
DR PIR; D88544; D88544.
DR PIR; S41041; S24462.
DR RefSeq; NP_001022705.2; NM_001027534.3. [P30645-1]
DR RefSeq; NP_001022706.2; NM_001027535.4. [P30645-3]
DR AlphaFoldDB; P30645; -.
DR SMR; P30645; -.
DR STRING; 6239.R08D7.6a; -.
DR iPTMnet; P30645; -.
DR EPD; P30645; -.
DR PaxDb; P30645; -.
DR PeptideAtlas; P30645; -.
DR EnsemblMetazoa; R08D7.6a.1; R08D7.6a.1; WBGene00011146. [P30645-1]
DR EnsemblMetazoa; R08D7.6b.1; R08D7.6b.1; WBGene00011146. [P30645-3]
DR GeneID; 176270; -.
DR KEGG; cel:CELE_R08D7.6; -.
DR UCSC; R08D7.6b; c. elegans. [P30645-1]
DR CTD; 176270; -.
DR WormBase; R08D7.6a; CE44867; WBGene00011146; pde-2. [P30645-1]
DR WormBase; R08D7.6b; CE44922; WBGene00011146; pde-2. [P30645-3]
DR eggNOG; KOG3689; Eukaryota.
DR GeneTree; ENSGT00940000159817; -.
DR HOGENOM; CLU_342318_0_0_1; -.
DR InParanoid; P30645; -.
DR OMA; RYDIEEP; -.
DR OrthoDB; 904682at2759; -.
DR PhylomeDB; P30645; -.
DR PRO; PR:P30645; -.
DR Proteomes; UP000001940; Chromosome III.
DR Bgee; WBGene00011146; Expressed in germ line (C elegans) and 4 other tissues.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005743; C:mitochondrial inner membrane; IBA:GO_Central.
DR GO; GO:0005759; C:mitochondrial matrix; IBA:GO_Central.
DR GO; GO:0005741; C:mitochondrial outer membrane; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IBA:GO_Central.
DR GO; GO:0097060; C:synaptic membrane; IBA:GO_Central.
DR GO; GO:0004115; F:3',5'-cyclic-AMP phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0047555; F:3',5'-cyclic-GMP phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0004114; F:3',5'-cyclic-nucleotide phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0004118; F:cGMP-stimulated cyclic-nucleotide phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042803; F:protein homodimerization activity; IBA:GO_Central.
DR GO; GO:0019933; P:cAMP-mediated signaling; IBA:GO_Central.
DR GO; GO:0046069; P:cGMP catabolic process; IBA:GO_Central.
DR GO; GO:0019934; P:cGMP-mediated signaling; IBA:GO_Central.
DR GO; GO:0007635; P:chemosensory behavior; IGI:UniProtKB.
DR GO; GO:0006935; P:chemotaxis; IGI:UniProtKB.
DR GO; GO:0008340; P:determination of adult lifespan; IGI:UniProtKB.
DR GO; GO:0043951; P:negative regulation of cAMP-mediated signaling; IBA:GO_Central.
DR GO; GO:0010754; P:negative regulation of cGMP-mediated signaling; IGI:UniProtKB.
DR GO; GO:1902160; P:negative regulation of cyclic nucleotide-gated ion channel activity; IGI:WormBase.
DR GO; GO:0007602; P:phototransduction; IGI:UniProtKB.
DR GO; GO:0010753; P:positive regulation of cGMP-mediated signaling; IMP:WormBase.
DR GO; GO:0010628; P:positive regulation of gene expression; IGI:UniProtKB.
DR GO; GO:0040018; P:positive regulation of multicellular organism growth; IMP:UniProtKB.
DR GO; GO:1901046; P:positive regulation of oviposition; IMP:UniProtKB.
DR GO; GO:0010821; P:regulation of mitochondrion organization; IBA:GO_Central.
DR GO; GO:0040014; P:regulation of multicellular organism growth; IGI:UniProtKB.
DR GO; GO:0046662; P:regulation of oviposition; IGI:UniProtKB.
DR GO; GO:0010446; P:response to alkaline pH; IGI:UniProtKB.
DR GO; GO:0042542; P:response to hydrogen peroxide; IGI:UniProtKB.
DR GO; GO:0070482; P:response to oxygen levels; IMP:WormBase.
DR GO; GO:0007165; P:signal transduction; IBA:GO_Central.
DR CDD; cd00077; HDc; 1.
DR Gene3D; 1.10.1300.10; -; 1.
DR Gene3D; 3.30.450.40; -; 1.
DR InterPro; IPR003018; GAF.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR023088; PDEase.
DR InterPro; IPR002073; PDEase_catalytic_dom.
DR InterPro; IPR036971; PDEase_catalytic_dom_sf.
DR InterPro; IPR023174; PDEase_CS.
DR Pfam; PF01590; GAF; 1.
DR Pfam; PF00233; PDEase_I; 1.
DR PRINTS; PR00387; PDIESTERASE1.
DR SMART; SM00065; GAF; 1.
DR SMART; SM00471; HDc; 1.
DR PROSITE; PS00126; PDEASE_I_1; 1.
DR PROSITE; PS51845; PDEASE_I_2; 1.
PE 3: Inferred from homology;
KW Alternative splicing; cGMP; Hydrolase; Metal-binding; Reference proteome.
FT CHAIN 1..831
FT /note="Probable 3',5'-cyclic phosphodiesterase pde-2"
FT /id="PRO_0000198845"
FT DOMAIN 177..312
FT /note="GAF"
FT DOMAIN 341..670
FT /note="PDEase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01192"
FT REGION 1..40
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 55..84
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 762..831
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..26
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 803..825
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 422
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 426
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 462
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 463
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 463
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 576
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT VAR_SEQ 48..50
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_014355"
SQ SEQUENCE 831 AA; 94364 MW; 0BCD803345E113B1 CRC64;
MLELRRNSSP SSAHPSPQTN CQNSQRGDGL HHHHHEAASG STCCGGMTVF TGANAAKSSN
EPAGSASPTV WRKTSHPPLH FNNNETRNRN LQMQLKNRGT KDDWGASLRY DIEEPTSSGL
LELLPDVPIV RKLSRPLVKM DDQDDACSVA SNESDRTVLS PLVPMSIFDQ FLCLTNNLSA
LISCIIAEAK KNTEAEDYAV FLHDEDNKQM VLFNNETMLM TGKKFDMGYG IVGKVASTMR
TMNIRDVSRC PFFNEEIDEQ FSIKARNLIA FPLIDSSCSL IGVIVLYNKE NGFSRHDEKY
IKRFSYFVAN SIAHAILAKQ IEEVRTRIHM VEEFKIQGED AVIEEVDIMR LVNDPLRDWR
YFSQNFADFS FPPRSVGENH FHRASMMFFE DLGFSMLYKL NKRKLSYLVL RVSAGYRPVP
YHNWSHAFAV THFCWLTLRT DAIRRALSDM ERLSLLIACL CHDIDHRGTT NSFQMQSLQK
TPLSVLYSTE GSVLERHHFA QTIKLLQQEE CSILENLPAA DFRTIVNTIR EVILATDISA
HLRKQERIKT MISEGYNPMS FDHRYLLMCL VMTASDLSDQ AKNFHNAKRI AENIYLEFFA
QGDLELQLGV KPLEMMDRTN AYVPTVQIDF LFKIGVPVFQ LLASVVPEGR TTSEAIDANH
LCWVALDEEV RNNPSATNTL EYLRDENLER RIYDRVRKQD PRAAEIASKR FEPVYANGSV
PQTQDILDHR FDGYDKKYQI GCSGGQNQSN GKQQQIRSLQ KIRSKTSEDD ALLKPMDNGG
SVAASSTRRG SRTPRRLWRR ARQLISSMSS SCASCSPLPS RRQVSEDSES C
