ENZYME: EC 3.1.4.17

Reaction catalysed:

     Nucleoside 3',5'-cyclic phosphate
  +  H(2)O
 <=>
     nucleoside 5'-phosphate

Comment(s):

• Acts on 3',5'-cyclic AMP, 3',5'-cyclic dAMP, 3',5'-cyclic IMP, 3',5'-cyclic GMP and 3',5'-cyclic CMP.

Cross-Reference(s):

• KYOTO UNIVERSITY LIGAND CHEMICAL DATABASE: .

  ENTRY       EC 3.1.4.17
  NAME        3',5'-Cyclic-nucleotide phosphodiesterase
  CLASS       Hydrolases
              Acting on ester bonds
              Phosphoric diester hydrolases
  SYSNAME     3',5'-Cyclic-nucleotide 5'-nucleotidohydrolase
  REACTION    Nucleoside 3',5'-cyclic phosphate + H2O = Nucleoside 5'-phosphate
  SUBSTRATE   Nucleoside 3',5'-cyclic phosphate
              3',5'-Cyclic AMP
              3',5'-Cyclic dAMP
              3',5'-Cyclic IMP
              3',5'-Cyclic GMP
              3',5'-Cyclic CMP
              H2O
  PRODUCT     Nucleoside 5'-phosphate
              AMP
              dAMP
              IMP
              GMP
              CMP
  COMMENT     Act on 3',5'-cyclic AMP, 3',5'-cyclic dAMP, 3',5'-cyclic IMP,
              3',5'-cyclic GMP and 3',5'-cyclic CMP.
  PATHWAY     PATH: MAP00230  Purine metabolism
  MOTIF       PS: PS00126  H-D-[LIVMFY]-x-H-x-[AG]-x(2)-[NQ]-x-[LIVMFY]
              PS: PS00607  H-x-H-L-D-H-[LIVM]-x-[GS]-[LIVMA]-[LIVM](2)-x-S-[AP]
  STRUCTURES  PDB: 1LOI  
  

  ---

  E.C. number	3.1.4.17 (BRENDA )
  Systematic name	3',5'-Cyclic-nucleotide 5'-nucleotidohydrolase
  Recommended name	3',5'-Cyclic-nucleotide phosphodiesterase
  Other names	3',5'-Cyclonucleotide phosphodiesterase Cyclic 3',5'-mononucleotide phosphodiesterase PDE <24> Phosphodiesterase, cyclic 3',5'-nucleotide Cyclic 3',5'-phosphodiesterase 3',5'-Nucleotide phosphodiesterase 3', 5'-Cyclic nucleoside monophosphate phosphodiesterase Cyclic 3',5'-nucleotide phosphodiesterase Cyclic 3',5-nucleotide monophosphate phosphodiesterase Cyclic nucleotide phosphodiesterase Nucleoside-3',5-monophosphate phosphodiesterase Nucleoside 3',5'-cyclic phosphate diesterase 3':5'-Cyclic nucleotide 5'-nucleotidohydrolase <24> Cytidine 3' :5'-monophosphate (cyclic CMP) phosphodiesterase <35> 3': 5'-Monophosphate (cyclic CMP) phosphodiesterase
  Common Names
  Reaction catalysed	Nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate
  Reaction type	Phosphoric ester hydrolysis
  Substrate spectrum	1.  Nucleoside 3',5'-cyclic phosphate + H2O <1-46> 2.  3',5'-cyclic AMP + H2O <1-6, 8-10, 12, 13, 15, 18, 19, 23, 24, 25, 27, 35, 38, 43, 44> 3.  3',5'-cyclic dAMP+ H2O 4.  3',5'-cyclic IMP + H2O <19, 20, 38> 5.  3',5'-cyclic GMP + H2O <1, 4, 6, 8, 9, 10, 12, 13, 15, 18, 19, 20, 23, 24, 25, 27, 35, 38, 43, 44> 6.  3',5'-cyclic CMP + H2O (not <1>) 7.  Deoxyribonucleoside 3',5'-cyclic phosphates + H2O <1> 8.  Tubercidin 3',5'-cyclic phosphate + H2O <1> 9.  N6-Etheno-cAMP + H2O <8> 10.  Cyclic 3',5'-UMP + H2O <19, 20, 38> 11.  Cyclic 3',5'-TMP + H2O <19, 20, 38> 12.  Dibutyryl cyclic AMP + H2O <19> 13.  N6-Monobutyryl-cAMP + h2O <38> 14.  More (not: 2',3'-cAMP <23, 25>, single enzyme with cyclic 2',3'and cyclic 3',5'-nucleotide diesterase activity <46, 41, 43>) <23, 25, 46, 41, 43>
  Products	1.  Nucleoside 5'-phosphate <1-47> 2.  5'-AMP (Latuca sativa: 3'- and 5'-AMP released from cyclic 3',5'-cAMP, 5'-nucleotide is major product <44>) 3.  5'-dAMP 4.  5'-IMP 5.  5'-GMP 6.  5'-CMP 7.  Deoxyribonucleoside 5'-phosphate 8.  Tubercidin 5'-phosphate 9.  ? 10.  5'-UMP 11.  5'-TMP 12.  ? 13.  ? 14.  ?
  Natural substrates	3',5'-cAMP (regulation of intracellular level of 3',5'-cAMP) <1>
  Turnover number (1/min)	34000 (cAMP, stimulation with Mg2+ or Mn2+) <18> 40000 (cGMP, stimulation with Mg2+ or Mn2+) <18> -999 <18>
  Specific activity (micromol/min/mg)	0.096 <6> 0.85 <22> 1.33 <18> 0.119 <24> 0.727 <25> -999 <1, 11, 13, 14, 16, 19, 21, 29, 35, 38, 39, 40, 41, 48>
  Km value (mM)	0.10 (cGMP, particulate enzyme, mouse) <10> 0.005 (cGMP, Xenopus laevis) <11> 0.030 (cAMP, Xenopus laevis <11>, cGMP, soluble, mouse <10>) <10, 11> 0.182 (cCMP) <35, 48> 0.0018 (cAMP) <6> 0.0020 (cGMP) <6> 0.090 (cAMP, particulate enzyme, mouse) <10> 0.125 (cAMP, soluble enzyme, mouse) <10> -999 (cGMP-specific enzymes: 50-fold selecticity towards cGMP as substrate, defined as ratio Vmax/Km for cGMP as compared to Vmax/KM for cAMP <3>, complex kinetics with 2 KM values <9, 19>) <2, 3, 4, 5, 12, 13, 14, 17, 18, 19, 20, 21, 24, 25, 27, 33, 34, 35, 37, 38, 39, 42, 44, 46>
  pH optimum	7.0-7.5 (Rhizobium fredii) <6> 9.0 <17> 8.5 <5, 20> 8.0 <2, 19> 7.0 <25, 35> 3.2-4.0 <46> 6.1 <48> 8.2 <40> 5.4-6.0 <43>
  pH range	7.0-9.0 (7.0: 37% of maximum activity, 9.0: optimum) <17> 5.5-11.5 <19>
  Temperature optimum (deg.C)	30 <20> 55 <17> 45 <19, 41>
  Temperature range (deg.C)	37-55 (55°C: optimum, 37°C: 45% of maximum activity) <17> 2-45 (45°C: optimum, 2°C: 10% of maximum activity, 30°C: 50% of maximum activity) <19> -999 <41>
  Cofactors/prosthetic groups	More (Ca2+/calmodulin stimulated enzyme type <3, 4, 26, 28, 29>, cGMP stimulated enzyme type <3>) <3, 4, 26, 28, 29>
  Metal ions/salts	Mg2+ (dependent on <1, 2>, required /Ca2+-dependent enzyme <4>, required <12>, stimulates <17, 18, 19, 20, 24, 35, 38, 39, 42>, slight stimulation <40>, Mn2+ and Co2+ may replace Mg2+ <4>) <1, 2, 4, 12, 17, 18, 19, 20, 24, 35, 38, 39, 42> Ca2+ (Sr2+, Ba2+, Co2+ may replace Ca2+ <4>, Ca2+/calmodulin stimulates enzymes of Ca2+/calmodulin stimulated type) <3, 4, 6, 11, 13, 15, 17, 26, 27, 28, 29, 33, 35> Ba2+ (stimulates) <6, 17> Mn2+ (or Mg2+ required, stimulates) <12, 17, 18, 19, 20, 24, 35, 39, 42, 42> Ni2+ (stimulates) <17, 42> Co2+ (stimulates) <17, 18, 19, 24, 39, 42, 43> Al3+ (stimulates) <17> Fe3+ (stimulates) <17, 44> Zn2+ (stimulates <24, 38, 43>, contains bound zinc, 2 atoms per subunit <32>, removal of Zn2+ causes reversible loss of activity) <24, 32, 38, 43> Cd2+ (stimulates) <17> Fe2+ (stimulates) <17, 24> K+ (stimulates) <17> Cs+ (stimulates) <17> Na+ (stimulates) <17> Cu2+ (stimulates) <17, 25> More (divalent metal required <1, 19, 20>, no metal ion required <6, 25, 41>, active in absence of added metal <24>) <1, 6, 19, 20, 24, 25, 41>
  Inhibitors	Zn2+ <1, 6, 23, 35, 41, 42> Theophylline (no effect <43>) <1, 14, 39, 41> Caffeine (no effect <43>) <1, 14, 19, 21, 39, 41> ATP <1, 19, 20> CTP <1> UTP <1> CuCl2 <38> ITP <1> diphosphate <1, 20> Puromycin <1> 3,3',5'-Triiodo-L-thyronine <1> Fe2+ <6, 35, 42> Fe3+ <6> Al3+ <6> Ca2+ <9, 23> Mn2+ <23, 41> Cu2+ <23, 41, 42, 44> Theobromine <39> Morin <16> L-Cysteine <16> Dimethylaminopurine <39> Co2+ <20, 23, 35, 41> Ni2+ <23> Beta-mercaptoethanol <16> Chloropromazine <1, 10> p-Chloromercuribenzoate <14, 39> Ethacrynic acid <1> Chlorthalidone <1> Urea <41, 43> NaF <43> ZnCl2 <16> Ba2+ <23, 41> Acetazoleamide 1,10-Phenanthroline <38> Diazoxide <1> Methaxanthines <2, 3, 20, 39> 4-(3-Butoxy-4-methoxybenzyl)-2-imidazolidinone <2> 1-Ethyl-4-(isopropylidenehydrazine)-1H-pyrazole-(3,4-b)-pyridine-5-carboxylic acid ethyl ester hydrochloride <2> cGMP (cAMP hydrolysis, some enzymes of the low-KM-phosphodiestrase type <3>, no effect <15>) <3, 12, 19> Milrinone <3, 8> Cilostamide <3> Fenoximone <3> Calmodulin antagonists <8, 30> Inhibitor protein (from oocytes) <31> Cyclic 3',5'-IMP (cAMP hydrolysis) <19> Dibutyryl cyclic AMP (cAMP hydrolysis) <19> TPP <38> Trifluoperazine <8, 15, 33> Calmidazolium <8> Ethylene glycol bis(beta-aminoethyl ether)-N,N'-tetraacetic acid (soluble but not particulate form) <10> Dithiothreitol (reduced) <14, 16> N-(6-Aminohexyl)-5-chloro-1-naphtalenesulfonamide <10> cAMP (hydrolysis og cGMP) <10, 12> Papaverine <12, 20, 42> 3-Isobutyl-1-methylxanthine <12, 16> cIMP <14> Glutathione <14> 5,5-Dithiobis(2-nitrobenzoic acid) <39> Adenine <39> Adenosine <39> EDTA <19> NAD <25> NADP <25> FAD <25> Nucleoside triphosphates <19> PO43- <20> 6-Xanthines (alkylated) <42> Hydroxypurine <39> More (enzymes from different tissues differ considerably with respect to inhibition) <2>
  Organism (original)	Mammalia <1, 3, 8, 28, 47> Fasciola hepatica <1> Lumbricus terrestris <1> Fly <1> Dictyostelium discoideum <1, 14, 16, 38> E. coli <1> Bull <1, 2, 22, 27, 28, 29, 33, 34, 40, 42> Dog <1, 21> Cat <2> Animals <2> Yeast <32> Frog <2> Bovine (overview <4>, calf <18>) <4, 18> Pig (overview <4>) <4, 35> Algae <5> Rhizobium fredii <6, 25> Sheep <28> Neurospora crassa (single enzyme with cyclic 2 '-3'- and cyclic 3',5'-nucleotide phosphodiesterase activity <46>) <7, 9, 23, 46> Mouse <10> Xenopus laevis <11, 15, 31> Human (overview <4>) <4, 12, 19> Rat (2 soluble forms PI and PII <13>, overview <4>) <4, 13, 26, 37> Mycobacterium smegmatis <17> Chlamydomonas reinhardtii <17, 20> Streptoverticillium album <30> Latuca sativa (enzyme cleaves also 2',3'cyclic nucleotides <45>) <24, 44, 45> Spinacia oleracea <36, 48> Rabbit (overview <4>) <4, 39> Bombyx mori (one enzyme with cyclic 2',3'- and cyclic 3',5 '-nucleotide phosphodiesterase activity) <41> Pisum sativum (one enzyme with cyclic 2',3'- and cyclic 3',5'-nucleotide phosphodiesterase activity) <43>
  Source	Cerebral cortex <1> Larvae (fly) <1> Liver <18, 37> Brain <1, 2, 27, 29, 40> Heart <1, 2, 21, 22, 42> Erythrocytes <2> Testis <26> Adrenal cortex tumor Y-1 cells <10> Platelets <12, 18> Pancreas <13> Oocytes <15> Leukocytes <19> Blood <18> Cotyledons <24, 44> Spermatozoa (epididymal) Adrenal medulla <34> Skeletal muscle <39> Photoreceptor <47> More (distribution of Ca2+/calmodulin dependent enzyme) <4>
  Localization	Peroxisomes <48> Chloroplast <48> Microsomes <36> More (at nerve endings in brain tissue <1>, Golgi fractions <48>) <1, 48>
  Purification	Rhizobium fredii <6, 24> Pig <35> Mouse <10> Dictyostelium discoideum <16, 38> Calf <18> Dog <21> Bull <22, 27-29, 40, 42> Yeast <32> Sheep <28> Neurospora crassa <7, 9, 46> Xenopus laevis <11> Human <12> Rat <13> Latuca sativa (partial) <24, 44> Spinacia oleracea <48> Rabbit <39> Bombyx mori (partial) <43> More (large scale) <29>
  Crystallization
  Molecular Weight	300000 (slime mold) <1> 200000 (rat liver) <1> 82000 (Rhizobium fredii MAR-1, gel filtration) <6> 58000-75000 (enzymes of Ca2+/calmodulin dependent type) <3> 102000-105000 (bovine cardiac cGMP stimulated enzyme, hydrodynamic measurements, gel electrophoresis) <3> 83000 (gel filtration in presence of EGTA, monomer, Neurospora crassa) <9> 151000 (gel filtration in presence of EGTA, dimer, Neurospora crassa) <9> 330000-400000 (gel filtration in presence of EGTA, tetramer, Neurospora crassa) <9> 350000 (Pisum sativum) <43> 140000 (gel filtration, Xenopus laevis <11>, gel filtration, human <12>) <11, 12> 175000 (polyacrylamide-gradient-gel electrophoresis, rat, PI) <13> 116000 (polyacrylamide-gradient-gel electrophoresis, rat, PII) <13> 55000 (gel filtration, Dictyostelium discoideum, MW 55000 and 150000-200000) <16> 150000-200000 (Dictyostelium discoideum, gel filtration, MW 55000 and 150000-200000) <16> 102000 (SDS-PAGE, calf) <18> 201000 (sedimentation coefficient, Stokes radius, calf) <18> 72000 (Latuca sativa, gel filtration) <24> 57000 (gel filtration, Rhizobium fredii) <25> 59000 (SDS-PAGE, bovine) <28> 216000 (gel filtration, bovine, Ca2+-independent cGMP-specific enzyme) <34> 230000 (gel filtration, bovine, cGMP stimulated enzyme) <34> 33000 (SDS-PAGE, pig) <35> 400000 (gel filtration, rat) <37> 66000 (sedimentation constant, Stokes radius, Bombyx mori) <41> 125000 (analytical ultracentrifugation, sucrose density-gradient centrifugation, bovine) <42> 250000 (gel filtration, bovine) <42> -999 <3, 27, 28, 42>
  Subunits	Dimer (most forms of Ca2+/calmodulin dependent enzyme type exist as dimer of approximately 120000, gel filtration, sucrose density gradient studies <3>, SDS-PAGE, 2 * 61000, human <12>, SDS-PAGE, 2 * 59000, bovine <28>) <3, 12, 28> Oligomer (SDS-PAGE, Rhizobium fredii, x * 28000 <6>, SDS-PAGE, Xenolus laevis, x * 66000 <11>, x * 55000, Dictyostelium discoideum, two forms, monomeric and oligomeric <16>) <6, 11, 16> Monomer (Rhizobium fredii <25>, 1 * 55000, Dictyostelium discoideum, two forms, monomeric and oligomeric, SDS-PAGE <16>) <16, 25> -999 <3>
  Glyco-/Lipoprotein
  Cross-refs to NBRF/PIR
  Cloned
  Cross-refs to Brookhaven
  pH stability	5.0-10 (below 5.0: irreversible denaturation, up to 10: 1 h at 0°C with little loss of activity) <2> 5.4 (quite stable at 4°C or-20°C) <43>
  Temperature stability (deg.C)	55 (purified enzyme inactivated much faster than less purified <4>, 10 min, 20% loss of activity <17>, 5 min, absence of cAMP, 50% loss of activity <19>) <4, 17, 19> 28 (80% of activity remaining after 7 days <6>, stable for at least 10 days <25>) <6, 25> 60 (20 min, no loss of activity) <6> 70 (20 min, 20% loss of activity <6>, 10 min, more than 90% loss of activity <17>) <6, 17> 37 (stable for at least 24 h) <17> 95 (stable up to, Neurospora crassa) <23>
  Organic solvent stability
  Oxidation stability
  General stability	Ca2+ and calmodulin (stabilize in highly purified preparations, destabilize in less purified one) <4> Repeated freezing and thawing (loss of activity) <27> More (stablilty of Ca2+-dependent enzyme) <4>
  Storage stability	At-70°C or at-20°C, tris buffer, pH 8.0, serum albumin, (stable for 9 months), 0-4°C (40% loss of activity after 1 month) <2> -70°C, 15% glycerol, 5 mg/ml ovalbumin (stable for at least 4 months) <18> -20°C, 2 months (20% loss of activty), 5 months (50% loss of activity) <19> More (stability of Ca2+-dependent enzyme <4>) <4, 27, 39, 43>
  Renaturated
  References	1.  Drummond, G.I., Yamamoto, M. in "The Enzymes" ,3rd Ed. (Boyer, P.D., eds) 4, 355-371 (1971) (Review) <2> Chasin, M., Harris, D.N.: Methods Mol. Biol.,3,169-198 (1972) (Review) 3 .   Beavo, J.A.: Adv. Second Messenger Phosphoprotein Res., 22, 1-38 (1988) (Review) 4.  Lin, Y.M., Cheung, W.Y. in "Calcium Cell Funct." (Cheung, W.Y., ed.) 1, 79-107, Academic New York, N.Y. (1980) (Review) 5 .   Amrhein, N.: Z. Pflanzenphysiol., 72, 249-261 (1974) 6 .   Lim, S.T., Krishnan, A.K., Ong, K.K.: Biochim. Biophys. Acta, 991, 353-358 (1989) 7 .   Ulloa, R.M., Rubinstein, C.P., Molina, L., Torres, H. N., Tellez-Inon, M.T.: FEBS Lett., 241, 219-222 (1988) 8 .   Kincaid, R.L., Manganiello, V.C.: Methods Enzymol., 159, 457-470 (1988) 9 .   Shaw, N., Harding, R.W.: Phytochemistry, 27, 1281-1288 (1987) 10 .   Ryan, J.A., Toscano, W.A.: Arch. Biochem. Biophys., 241, 403-412 (1985) 11 .   Orellana, O., Jedlicki, E., Allende, C.C., Allende, J.E.: Arch. Biochem. Biophys., 231, 345-354 (1984) 12 .   Grant, P.G., Colman, R.W.: Biochemistry, 23, 1801-1807 (1984) 13 .   Vandermeers, A., Vandermeers-Piret, M.-C., Rathe, J., Christophe, J.: Biochem. J., 211, 341-347 (1983) 14 .   Yamasaki, F., Hayashi, H.: J. Biochem., 91, 981-988 (1982) 15 .   Miot, F., Erneux, C.: Biochim. Biophys. Acta, 701, 253-259 (1982) 16 .   Orlow, S.J., Shapiro, R.I., Franke, J., Kessin, R.H.: J. Biol. Chem., 256, 7620-7627 (1981) 17 .   Lee, C.H.: J. Gen. Microbiol., 107, 177-181 (1978) 18 .   Yamamoto, T., Manganiello, V.C., Vaughan, M.: J. Biol. Chem., 258, 12526-12533 (1983) 19 .   Song, S.-Y., Cheung, W.Y.: Biochim. Biophys. Acta, 242, 593-605 (1971) 20 .   Fischer, U., Amrhein, N.: Biochim. Biophys. Acta, 341, 412-420 (1974) 21 .   Nair, K.G.: Biochemistry, 5, 150-157 (1966) 22 .   Butcher, R.W.: Methods Enzymol., 38, 218-223 (1974) 23 .   Shaw, N.M., Harding, R.W.: FEBS Lett., 152, 295-298 (1983) 24 .   Chiatante, D., Newton, R.P., Brown, E.G.: Biochem. Soc. Trans., 13, 1133-1134 (1985) 25 .   Lim, S.T., Palanisamy, U.M., Ong, K.K.: Arch. Microbiol., 146, 142-146 (1986) 26 .   Purvis, K., Rui, H.: Methods Enzymol., 159, 675-685 (1988) 27 .   Sharma, R.K., Wang, J.H.: Methods Enzymol., 159, 582-594 (1988) 28 .   Kincaid, R.L., Vaughan, M.: Methods Enzymol., 159, 557-573 (1988) 29 .   Hansen, R.S., Charbonneau, H., Beavo, J.A.: Methods Enzymol., 159, 543-557 (1988) 30 .   Matsuda, Y., Asano, K., Kawamoto, I., Yasuzawa, T., Shirahata, K., Sano, H., Kase, H.: Agric. Biol. Chem., 52, 3211-3213 (1988) 31 .   Jedlicki, E., Allende, C., Allende, J.E.: Methods Enzymol., 159, 660-667 (1988) 32 .   Londesborough, J., Suoranta, K.: Methods Enzymol., 159, 777-785 (1988) 33 .   Chaudry, P.S., Casillas, E.R.: Arch. Biochem. Biophys., 262, 439-444 (1988) 34 .   Sabatine, J.M., Coffee, C.J.: Arch. Biochem. Biophys., 249, 95-105 (1986) 35 .   Helfman, D.M., Shoji, M., Kuo, J.F.: J. Biol. Chem., 256, 6327-6334 (1981) 36 .   Edwards, M., Brown, E.G., Newton, R.P., Smith, C.J.: Biochem. Soc. Trans., 5, 975-977 (1977) 37 .   Terasaki, W.L., Russell, T.R., Appleman, M.M.: methods Enzymol., 38, 257-259 (1974) 38 .   Chassy, B.M., Porter, E.V.: Methods Enzymol., 38, 244-248 (1974) <39> Kemp, R.G., Huang, Y.-C.: Methods Enzymol.,38, C,240-244 (1974) <40> Cheung, W.Y., Lin, Y.M.: Methods Enzymol.,38C,223-239 (1974) <41> Morishimna, I.: Biochim. Biophys. Acta,370,227-241 (1974) <42> Goren, E.N., Rosen, O.M.: Arch. Biochem. Biophys.,153,384-397 (1972) <43> Lin, P. P.-C., Varner, J.E.: Biochim. Biophys. Acta,276,454-474 (1972) <44> Chiatante, D., Newton, R.P., Brown, E.G.: Phytochemistry,25,1545-1551 (1986) <45> Chiatante, D., Newton, R.P., Brown, E.G.: Phytochemistry,26,1301-1306 (1987) <46> Hasunuma, K.: J. Bacteriol.,156,291-300 (1983) <47> Pannbacker, R.G., Fleischman, D.E., Reed, D.W.: Science,175,757-758 (1972) <48> Brown, E.G., Edwards, M.J., Newton, R.P., Smith, C.J. : Phytochemistry,18,1943-1948 (1979)