Q8MM62 (PDE6_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
cAMP/cGMP-dependent 3',5'-cAMP/cGMP phosphodiesterase B
EC=3.1.4.35
EC=3.1.4.53

Alternative name(s):
Cyclic GMP-binding protein B
Phosphodiesterase 6
Short name=DdPDE6
Phosphodiesterase E

Gene names

Name:	pdeE
Synonyms:	gbpB, pde6
ORF Names:	DDB_G0276027

Organism

Dictyostelium discoideum (Slime mold)

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1096 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Dual specificity cAMP and cGMP phosphodiesterase with marked preference for cyclic AMP, which is activated by cAMP and cGMP. Likely functions as a cAMP-stimulated cAMP-phosphodiesterase which may play a role in regulating the cAMP relay response. Ref.2 Ref.5 Ref.6
Catalytic activity	Adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate. Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
Cofactor	Divalent metal cation. Can use manganese and to a lower extent magnesium and zinc. Half-maximal activation occurs between 10 and 100 µM of manganese whereas maximal activation occurs with 10 mM of zinc or magnesium. Ref.2
Subcellular location	Cytoplasm › cytosol Probable Ref.5 Ref.7.
Developmental stage	Low expression during growth. Mainly expressed after 8-10 hours of starvation when cells are aggregating and in the multicellular stage. Ref.2 Ref.5 Ref.6
Domain	The beta lactamase-like domain catalyzes the hydrolysis of cGMP By similarity.
Sequence similarities	Belongs to the metallo-beta-lactamase superfamily. cNMP phosphodiesterase family. Contains 2 cyclic nucleotide-binding domains.
Biophysicochemical properties	Kinetic parameters: cAMP/cGMP selectivity of 9. KM=200 µM for cAMP Ref.5 Ref.6 KM=800 µM for cGMP Vmax=650 nmol/min/mg enzyme with cAMP as substrate Vmax=300 nmol/min/mg enzyme with cGMP as substrate pH dependence: Optimum pH is 7.0.

Ontologies

Keywords
Cellular component	Cytoplasm
Domain	Repeat
Ligand	Magnesium Manganese Metal-binding Nucleotide-binding Zinc cAMP cAMP-binding cGMP cGMP-binding
Molecular function	Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cAMP catabolic process Traceable author statement. Source: dictyBase cGMP catabolic process Traceable author statement. Source: dictyBase
Cellular component	cytosol Inferred from electronic annotation. Source: UniProtKB-SubCell extracellular space Inferred from direct assay. Source: dictyBase
Molecular function	3',5'-cyclic-AMP phosphodiesterase activity Traceable author statement. Source: dictyBase 3',5'-cyclic-GMP phosphodiesterase activity Traceable author statement. Source: dictyBase cAMP binding Inferred from electronic annotation. Source: UniProtKB-KW cGMP binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1096	1096	cAMP/cGMP-dependent 3',5'-cAMP/cGMP phosphodiesterase B		PRO_0000353106
Regions
	Nucleotide binding	783 – 930	148	cNMP 1
	Nucleotide binding	946 – 1070	125	cNMP 2
	Compositional bias	214 – 218	5	Poly-Ser
	Compositional bias	241 – 245	5	Poly-Gln
	Compositional bias	457 – 460	4	Poly-Ser
Sites
	Metal binding	573	1	Divalent metal cation Potential
	Metal binding	575	1	Divalent metal cation Potential
	Metal binding	577	1	Divalent metal cation Potential

Sequences

	Sequence		Length	Mass (Da)
	Q8MM62 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: 4F4F8CF199223782	FASTA	1,096	124,924
	10 20 30 40 50 60 MNSKYGDNII DFLRYLEKFV KSLTKDNKIE EFKTFDIKSL LYPRNKDYFG NLSKFLLAVI 70 80 90 100 110 120 SARIGSNFIN EDDIFEISEL LKEFLGQELE HLPYLSYEEL YVEIVEQVGE INGTVSEIIE 130 140 150 160 170 180 AITVTIDFLD TFEKVSQTID RSNEKQKLLA YLSAPVNQLD NSVSGVFNEN DYTDIQRFFT 190 200 210 220 230 240 ELTNENNQSP DSNISILIND FQSLLNILES QQASSSSSKM IINDSPRTQQ RNGTTEQQKK 250 260 270 280 290 300 QQQQQYLQKN KEPFYSKDKI MQVSGPSYVF TPSDCNVSIQ VGIPPDTLKR DQSICHFIVP 310 320 330 340 350 360 HFLISKDVSL SEVEFPIFYN KFVQKGKTKV VIICTVEQKQ RIETILCESI FGPAPEHIYT 370 380 390 400 410 420 DEEITIPDYK IDLLTERLAI DPRANDEKLD SYVIFKTFDT FGVVDIDLPS ASDPTKLINL 430 440 450 460 470 480 RIRNTKGLIS FHEDYHVVQK QLHLKLQEQQ QDQQDKSSSS TTDKQMINTS GNRIILKNNT 490 500 510 520 530 540 VSVIDSTIES QYVPVLPFGN DHEQVKKFKA PILGVTFLGV SHGLDFTHCS HTTGFIIWIN 550 560 570 580 590 600 GSGVVVDPPV GNTTYLQTNG IYGKTVEHII LTHCHADHDS GILQKIIERN KVTLYTTKTI 610 620 630 640 650 660 NESYMRKLKA LTGLPEQSLK NYYTWVPVTI GNKIKILGAE FEFDYSFHVI PTIRFKLEIY 670 680 690 700 710 720 NKKISYSADT FYDLQKFKQL KDQGVLSKKR IERLKSFVFD ADMIIHESGV APIHTPMANL 730 740 750 760 770 780 LELPSEIRKK IRVVHCSSSV DTKGEIIRPK EGLENTEIIK VDRKYKGVAE CIQIQTALNH 790 800 810 820 830 840 CSVFSKLSPA EVQRVFFLCK KIWVKRNDVI IKKGSPSDMF YIILSGKVLV YENEYEPIKS 850 860 870 880 890 900 TTSVGTVVTD TTTITTTVKT DAIKIPTIKL CAGETLGESA LQLDKNIDAS ATVIAETDVC 910 920 930 940 950 960 LLVWKTMDLR TEFHSNLNTF ISKVHMDLSH INSCRDAIIR AFQHNITQHI NKEEVDSIAN 970 980 990 1000 1010 1020 GSKDVSFAHH QVIFNEGDTS DSMYIIKQGR VRIHSKKNKN IIRYLNVGDF FGETAYRRSN 1030 1040 1050 1060 1070 1080 EDSNFLPTRS FTATAIDPTI LLKLDIESIV NPRIQNIIEQ KAKKNAEDNI RYHAYSPKIR 1090 TPRTPRKVYP IEGLSI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of four candidate cGMP targets in Dictyostelium." Goldberg J.M., Bosgraaf L., Van Haastert P.J.M., Smith J.L. Proc. Natl. Acad. Sci. U.S.A. 99:6749-6754(2002) [PubMed: 12011437] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Characterization of a cAMP-stimulated cAMP phosphodiesterase in Dictyostelium discoideum." Meima M.E., Weening K.E., Schaap P. J. Biol. Chem. 278:14356-14362(2003) [PubMed: 12574165] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, DEVELOPMENTAL STAGE, COFACTOR.
[3]	"Sequence and analysis of chromosome 2 of Dictyostelium discoideum." Gloeckner G., Eichinger L., Szafranski K., Pachebat J.A., Bankier A.T., Dear P.H., Lehmann R., Baumgart C., Parra G., Abril J.F., Guigo R., Kumpf K., Tunggal B., Cox E.C., Quail M.A., Platzer M., Rosenthal A., Noegel A.A. Nature 418:79-85(2002) [PubMed: 12097910] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.
[4]	"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: 15875012] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.
[5]	"A novel cGMP signalling pathway mediating myosin phosphorylation and chemotaxis in Dictyostelium." Bosgraaf L., Russcher H., Smith J.L., Wessels D., Soll D.R., Van Haastert P.J.M. EMBO J. 21:4560-4570(2002) [PubMed: 12198158] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, DEVELOPMENTAL STAGE.
[6]	"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: 12429832] [Abstract] Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, DEVELOPMENTAL STAGE.
[7]	"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: 17040207] [Abstract] Cited for: SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF481922 Genomic DNA. Translation: AAM34040.1. AY047364 Genomic DNA. Translation: AAL06060.1. AAFI02000014 Genomic DNA. Translation: EAL69313.1.
RefSeq	XP_643272.1. XM_638180.1.
3D structure databases
ProteinModelPortal	Q8MM62.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0185220; DDB0185220; DDB_G0276027.
GeneID	8620315.
GenomeReviews	Gene locus pdeE in contig CM000151_GR.
KEGG	ddi:DDB_G0276027.
Organism-specific databases
dictyBase	DDB_G0276027. pdeE.
Phylogenomic databases
eggNOG	NOG70621.
GeneTree	EPrGT00050000003837.
ProtClustDB	CLSZ2430915.
Family and domain databases
InterPro	IPR001279. Beta-lactamas-like. IPR018490. cNMP-bd-like. IPR000595. cNMP-bd_dom. IPR014710. RmlC-like_jellyroll. [Graphical view]
Gene3D	G3DSA:2.60.120.10. RmlC-like_jellyroll. 2 hits.
Pfam	PF00027. cNMP_binding. 2 hits. [Graphical view]
SMART	SM00100. cNMP. 2 hits. SM00849. Lactamase_B. 1 hit. [Graphical view]
SUPFAM	SSF51206. cNMP_binding. 2 hits.
PROSITE	PS00888. CNMP_BINDING_1. False negative. PS00889. CNMP_BINDING_2. False negative. PS50042. CNMP_BINDING_3. 2 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PDE6_DICDI

Accession

Primary (citable) accession number: Q8MM62
Secondary accession number(s): Q552E1

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 25, 2008
Last sequence update:	October 1, 2002
Last modified:	September 21, 2011
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)