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cAMP-specific 3',5'-cAMP phosphodiesterase 4 (EC 3.1.4.53) (Phosphodiesterase 4) (DdPDE4)

 PDE4_DICDI              Reviewed;        1039 AA.
Q86H13; Q54HY3; Q54HY4;
10-FEB-2009, integrated into UniProtKB/Swiss-Prot.
30-NOV-2010, sequence version 2.
28-MAR-2018, entry version 95.
RecName: Full=cAMP-specific 3',5'-cAMP phosphodiesterase 4;
EC=3.1.4.53;
AltName: Full=Phosphodiesterase 4;
Short=DdPDE4;
Flags: Precursor;
Name=Pde4; ORFNames=DDB_G0289121;
Dictyostelium discoideum (Slime mold).
Eukaryota; Amoebozoa; Mycetozoa; Dictyostelids; Dictyosteliales;
Dictyosteliaceae; Dictyostelium.
NCBI_TaxID=44689;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=AX4;
PubMed=15875012; DOI=10.1038/nature03481;
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.;
"The genome of the social amoeba Dictyostelium discoideum.";
Nature 435:43-57(2005).
[2]
NUCLEOTIDE SEQUENCE [MRNA] OF 283-1039, BIOPHYSICOCHEMICAL PROPERTIES,
CHARACTERIZATION, DEVELOPMENTAL STAGE, ENZYME REGULATION, FUNCTION,
TOPOLOGY, AND DISRUPTION PHENOTYPE.
PubMed=16644729; DOI=10.1074/jbc.M600040200;
Bader S., Kortholt A., Snippe H., Van Haastert P.J.M.;
"DdPDE4, a novel cAMP-specific phosphodiesterase at the surface of
dictyostelium cells.";
J. Biol. Chem. 281:20018-20026(2006).
[3]
SUBCELLULAR LOCATION.
PubMed=12429832; DOI=10.1091/mbc.E02-05-0302;
Bosgraaf L., Russcher H., Snippe H., Bader S., Wind J.,
Van Haastert P.J.M.;
"Identification and characterization of two unusual cGMP-stimulated
phoshodiesterases in dictyostelium.";
Mol. Biol. Cell 13:3878-3889(2002).
[4]
SUBCELLULAR LOCATION.
PubMed=17040207; DOI=10.1042/BJ20061153;
Bader S., Kortholt A., Van Haastert P.J.M.;
"Seven Dictyostelium discoideum phosphodiesterases degrade three pools
of cAMP and cGMP.";
Biochem. J. 402:153-161(2007).
-!- FUNCTION: Phosphodiesterase specific for extracellular cAMP.
Involved in the degradation of extracellular cAMP specifically
during multicellular development. {ECO:0000269|PubMed:16644729}.
-!- CATALYTIC ACTIVITY: Adenosine 3',5'-cyclic phosphate + H(2)O =
adenosine 5'-phosphate.
-!- COFACTOR:
Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
Evidence={ECO:0000250};
Note=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. {ECO:0000250};
-!- ENZYME REGULATION: Inhibited by 3-isobutyl-1-methylxanthine
(IBMX). {ECO:0000269|PubMed:16644729}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=10 uM for cAMP (catalytic domain expressed in vegetative AX2
cells) {ECO:0000269|PubMed:16644729};
Vmax=4200 pmol/min/mg enzyme with cAMP as substrate
{ECO:0000269|PubMed:16644729};
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Multi-pass
membrane protein {ECO:0000305}.
-!- DEVELOPMENTAL STAGE: Low expression during growth and cell
aggregation (up to 6 hours), maximally increases after 9 hours of
starvation, during the mound stage. Remains expressed at
significant levels during the other stages of multicellular
development. {ECO:0000269|PubMed:16644729}.
-!- DISRUPTION PHENOTYPE: Null cells show a reduction of
phosphodiesterase activity on the cell surface. Aggregation speed
is similar, but from the mound stage until fruiting body formation
it is slower. Aggregates largely remain as mounds; after 15 hours
(compared to slugs in wild type cells), after 20 hours (compared
to culmination state in wild type cells) and after 27 hours
(compared to completion of fruiting body formation in wild type
cells). Thus, slug formation and culmination appear to be
affected. These processes were not only slower but also less slugs
and fruiting bodies are formed. {ECO:0000269|PubMed:16644729}.
-!- SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase
family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAO59486.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
Sequence=EAL62868.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=EAL62884.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AY211984; AAO59486.1; ALT_INIT; mRNA.
EMBL; AAFI02000130; EAL62868.1; ALT_SEQ; Genomic_DNA.
EMBL; AAFI02000130; EAL62884.1; ALT_SEQ; Genomic_DNA.
RefSeq; XP_636379.1; XM_631287.1.
RefSeq; XP_636380.1; XM_631288.1.
ProteinModelPortal; Q86H13; -.
STRING; 44689.DDB0216197; -.
PaxDb; Q86H13; -.
EnsemblProtists; EAL62868; EAL62868; DDB_G0289121.
EnsemblProtists; EAL62884; EAL62884; DDB_G0289153.
GeneID; 8626980; -.
GeneID; 8626981; -.
KEGG; ddi:DDB_G0289121; -.
KEGG; ddi:DDB_G0289153; -.
dictyBase; DDB_G0289121; pde4.
eggNOG; KOG3688; Eukaryota.
eggNOG; KOG3689; Eukaryota.
eggNOG; ENOG410XPUK; LUCA.
InParanoid; Q86H13; -.
KO; K13293; -.
PhylomeDB; Q86H13; -.
BRENDA; 3.1.4.53; 1939.
Reactome; R-DDI-165160; PDE3B signalling.
Reactome; R-DDI-418457; cGMP effects.
Reactome; R-DDI-418555; G alpha (s) signalling events.
SABIO-RK; Q86H13; -.
PRO; PR:Q86H13; -.
Proteomes; UP000002195; Chromosome 5.
Proteomes; UP000002195; Unassembled WGS sequence.
GO; GO:0005576; C:extracellular region; TAS:dictyBase.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0005886; C:plasma membrane; IDA:dictyBase.
GO; GO:0004115; F:3',5'-cyclic-AMP phosphodiesterase activity; IMP:dictyBase.
GO; GO:0030552; F:cAMP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006198; P:cAMP catabolic process; IMP:dictyBase.
GO; GO:0031000; P:response to caffeine; IDA:dictyBase.
GO; GO:0007165; P:signal transduction; IEA:InterPro.
GO; GO:0030587; P:sorocarp development; IMP:dictyBase.
CDD; cd00077; HDc; 1.
Gene3D; 1.10.1300.10; -; 2.
InterPro; IPR003607; HD/PDEase_dom.
InterPro; IPR023088; PDEase.
InterPro; IPR002073; PDEase_catalytic_dom.
InterPro; IPR036971; PDEase_catalytic_dom_sf.
InterPro; IPR023174; PDEase_CS.
InterPro; IPR013706; PDEase_N.
Pfam; PF00233; PDEase_I; 1.
Pfam; PF08499; PDEase_I_N; 1.
PRINTS; PR00387; PDIESTERASE1.
PROSITE; PS00126; PDEASE_I_1; 1.
PROSITE; PS51845; PDEASE_I_2; 1.
1: Evidence at protein level;
cAMP; cAMP-binding; Cell membrane; Coiled coil; Complete proteome;
Glycoprotein; Hydrolase; Membrane; Metal-binding; Nucleotide-binding;
Reference proteome; Signal; Transmembrane; Transmembrane helix.
SIGNAL 1 29 {ECO:0000255}.
CHAIN 30 1039 cAMP-specific 3',5'-cAMP
phosphodiesterase 4.
/FTId=PRO_0000363970.
TOPO_DOM 30 201 Extracellular. {ECO:0000255}.
TRANSMEM 202 222 Helical. {ECO:0000255}.
TOPO_DOM 223 226 Cytoplasmic. {ECO:0000255}.
TRANSMEM 227 247 Helical. {ECO:0000255}.
TOPO_DOM 248 256 Extracellular. {ECO:0000255}.
TRANSMEM 257 277 Helical. {ECO:0000255}.
TOPO_DOM 278 283 Cytoplasmic. {ECO:0000255}.
TRANSMEM 284 304 Helical. {ECO:0000255}.
TOPO_DOM 305 310 Extracellular. {ECO:0000255}.
TRANSMEM 311 331 Helical. {ECO:0000255}.
TOPO_DOM 332 356 Cytoplasmic. {ECO:0000255}.
TRANSMEM 357 377 Helical. {ECO:0000255}.
TOPO_DOM 378 1039 Extracellular. {ECO:0000255}.
DOMAIN 533 973 PDEase. {ECO:0000255|PROSITE-
ProRule:PRU01192}.
COILED 384 414 {ECO:0000255}.
COMPBIAS 45 63 Poly-Asn.
COMPBIAS 122 157 Poly-Asn.
COMPBIAS 160 179 Poly-Asn.
COMPBIAS 485 491 Poly-Asn.
COMPBIAS 497 501 Poly-Asn.
COMPBIAS 748 756 Poly-Ser.
COMPBIAS 771 785 Poly-Thr.
COMPBIAS 786 796 Poly-Asn.
COMPBIAS 988 1009 Poly-Gln.
ACT_SITE 609 609 Proton donor. {ECO:0000255|PROSITE-
ProRule:PRU01192}.
METAL 613 613 Divalent metal cation 1.
{ECO:0000255|PROSITE-ProRule:PRU01192}.
METAL 648 648 Divalent metal cation 1.
{ECO:0000255|PROSITE-ProRule:PRU01192}.
METAL 649 649 Divalent metal cation 1.
{ECO:0000255|PROSITE-ProRule:PRU01192}.
METAL 649 649 Divalent metal cation 2.
{ECO:0000255|PROSITE-ProRule:PRU01192}.
METAL 861 861 Divalent metal cation 1.
{ECO:0000255|PROSITE-ProRule:PRU01192}.
CARBOHYD 11 11 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 34 34 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 37 37 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 119 119 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 124 124 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 131 131 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 167 167 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 178 178 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 406 406 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 430 430 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 500 500 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 515 515 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 769 769 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 791 791 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 795 795 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 804 804 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 809 809 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 823 823 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 826 826 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 874 874 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 944 944 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 1018 1018 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 1023 1023 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CONFLICT 284 284 Y -> D (in Ref. 2; AAO59486).
{ECO:0000305}.
SEQUENCE 1039 AA; 119447 MW; 29817E88B3B3ADD6 CRC64;
MFNNNNNDKI NNTMMSNNPS GQIINLESID CNSNLSNTTS IKDSNNNNNN NNNNNNNINN
NINKINPNID RKVLDDFNSK SIKIIDNKLN KKNSKKNLYS KEVDDDINKI NLNKKIIPNE
TNSNNSNNNN NNSNNNNNNN NNNNNFNYNN NINSNNNIIN NNNNINNNSN NNNNNNNNNS
ISLYVDTQEK SKKKVNAESL RGPIIFQNFI LYTFFLIVIG TAEGTSWAPE IRVANFVPYC
VMCVVLLEFN RLHKKPLLRI IFPLYTSNIP FAYMCIFSRE ARKYVLISLL FFASCLCIFL
QSGIPDLRKH IVIFCIIFMI NYGCCILFMD WFYIDTTGTK PYRGRILATK IHWGEEATIL
VSMALLGCIF IVLEKFIKSY ARCVAEQHYQ IQCLQKEKEK LQTEINISLK KLDLDTPIEK
IMDILRSMIN TSESENDKKQ LIKVIAVLGS NKLYDPDFKF ETCTDDAEVY SWLQSMLNRE
VGYSNVNNNN NMMMIENNNN NTIINNNLIE PTSPNFSKKL TSSDLIPRIR SMPEITDQGI
QELIINNFLE WDFPVFQLSE ITDGNPLFYM SYFLFSRHKF FEKFKIGIDC FKNFMRKIES
GYDSTNPYHN SIHATDVLHN LNYFIEKSFG KFLTDIELFS MILAAIIHDF KHPGVNNHFQ
INSKSRLALK YNDKSILENY HLHQAFIIMN EPESGILLKL SDSVRKEIRE TIIALVLSTD
MAKHFNLVGR FKSMANSFPT TTNTQQPSSS SSSSSSTTIP TSTITPTPNS TTSTTTTTTT
TTTTTNNNNN NNSNNNSLNN IINNCSSSNG SMGASGADNS NSNNTNNSNS NNQNQCGSSI
FLNSNKKDRL LLMKISIKCA DISNPSKPWN LYTNWSNRVT SEFYKQGDKE KESNMDVSAF
MDRNKPATTK CQINFINIFV APIYEIWSHH FPQFKLCYQN ILSNLSRLEI EQQQQLQLQQ
QQQQQLQQQQ QQQQQIHQQQ QQQLHHHQQQ QQFQHQQHQQ QLQHQHQQQL NNQNQNQNQS
NSNNSNSFGL TQSNYLIVV


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