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Literature summary extracted from

  • Kimura, Y.; Okazaki, N.; Takegawa, K.
    Enzymatic characteristics of two novel Myxococcus xanthus enzymes, PdeA and PdeB, displaying 3',5'- and 2'3'-cAMP phosphodiesterase, and phosphatase activities (2009), FEBS Lett., 583, 443-448.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.1.4.16 expressed in Escherichia coli BL21 cells Myxococcus xanthus
3.1.4.17 expressed in Escherichia coli pG-Tf2/BL21 cells Myxococcus xanthus
3.1.4.53 expressed in Escherichia coli BL21 cells Myxococcus xanthus

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.1.4.16 phosphate PdeB is strongly inhibited by 0.1 M sodium phosphate buffer (pH 6.0 and 7.0) Myxococcus xanthus
3.1.4.16 Zn2+ 28% relative activity at 0.05 mM Zn2+, using cyclic 3',5'-AMP as substrate Myxococcus xanthus
3.1.4.17 Co2+ PdeA and PdeB are inhibited (20-30%) at 0.25 mM Co2+ Myxococcus xanthus
3.1.4.17 EDTA PdeA and PdeB show 39% relative activity in the hydrolysis of 3',5'-cAMP in the presence of 0.05 mM EDTA Myxococcus xanthus
3.1.4.17 Mn2+ PdeA and PdeB are inhibited (20-30%) at 0.25 mM Mn2+ Myxococcus xanthus
3.1.4.17 additional information PdeA and PdeB are not stimulated by 3-isobuthyl-1-methylxanthine, theophylline, beta-glycerophosphate, Ca2+, Mg2+, Fe2+, and Fe3+ Myxococcus xanthus
3.1.4.17 orthovanadate PdeA shows 26% relative activity and PdeB shows 29% relative activity in the hydrolysis of 3',5'-cAMP in the presence of 0.05 mM orthovanadate Myxococcus xanthus
3.1.4.17 phosphate PdeA and PdeB enzyme activities are strongly inhibited by 0.1 M sodium phosphate buffer (pH 6.0 and 7.0), the PdeB activity is more strongly inhibited by 0.1 M phosphate than is PdeA activity Myxococcus xanthus
3.1.4.17 phosphoserine PdeA shows 59% relative activity and PdeB shows 73% relative activity in the hydrolysis of 3',5'-cAMP in the presence of 0.05 mM phosphoserine Myxococcus xanthus
3.1.4.17 phosphotyrosine PdeA shows 44% relative activity and PdeB shows 52% relative activity in the hydrolysis of 3',5'-cAMP in the presence of 0.05 mM phosphotyrosine Myxococcus xanthus
3.1.4.17 Zn2+ PdeA and PdeB are potently inhibited in the hydrolysis of 3',5'-cAMP by 0.05 mM Zn2+ with 24% and 28% of remaining activity Myxococcus xanthus
3.1.4.53 EDTA PdeA and PdeB show 39% residual activity, respectively, for 3',5'-cAMP hydrolysis at 0.1 mM EDTA Myxococcus xanthus
3.1.4.53 additional information he 3',5'-phosphodiesterase activities of PdeA and PdeB are not inhibited by theophylline, 3-isobuthyl-1-methylxanthine, and beta-glycerophosphate Myxococcus xanthus
3.1.4.53 O-phospho-L-serine PdeA and PdeB show 59% and 73% residual activity, respectively, for 3',5'-cAMP hydrolysis at 5 mM phosphoserine Myxococcus xanthus
3.1.4.53 O-phospho-L-tyrosine PdeA and PdeB show 44% and 52% residual activity, respectively, for 3',5'-cAMP hydrolysis at 5 mM phosphotyrosine Myxococcus xanthus
3.1.4.53 orthovanadate PdeA and PdeB show 26% and 29% residual activity, respectively, for 3',5'-cAMP hydrolysis at 1 mM orthovanadate Myxococcus xanthus
3.1.4.53 Zn2+ the 3',5'-phosphodiesterase enzyme activities of PdeA and PdeB are reduced to 24% and 28%, respectively, by 0.05 mM Zn2+ at pH 8.0 in 50 mM Tris-HCl buffer Myxococcus xanthus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.4.16 0.0052
-
 cyclic 2',3'-AMP in 50 mM Tris-HCl, pH 8.0 Myxococcus xanthus
3.1.4.17 0.0014
-
 5'-AMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.0016
-
 5'-AMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.0033
-
 3',5'-cAMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.0033
-
 5'-ATP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.0038
-
 2',3'-cAMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.005
-
 3',5'-cAMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.0052
-
 2',3'-cAMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.0125
-
 5'-ATP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.53 0.0033
-
 3',5'-cAMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.53 0.005
-
 3',5'-cAMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.1.4.16 Co2+ PdeB is stimulated about 2fold by 0.05 mM Co2+, at pH 8.0 in 50 mM Tris-HCl buffer with cyclic 3',5'-AMP as substrate Myxococcus xanthus
3.1.4.16 Mn2+ PdeB is stimulated about 2fold by 0.05 mM Mn2+, at pH 8.0 in 50 mM Tris-HCl buffer with cyclic 3',5'-AMP as substrate Myxococcus xanthus
3.1.4.16 additional information enzymatic activity is not stimulated by Ca2+, Mg2+, Fe2+, Fe3+, and Zn2+ Myxococcus xanthus
3.1.4.17 Co2+ the enzyme activities of PdeA and PdeB in the hydrolysis of 3',5'-cAMP are stimulated 3.2fold and 1.98fold at pH 8.0 in 50 mM Tris-HCl buffer by the addition of Co2+ at 0.05 mM, respectively Myxococcus xanthus
3.1.4.17 Mn2+ the enzyme activities of PdeA and PdeB in the hydrolysis of 3',5'-cAMP are stimulated 4fold and 2.14fold at pH 8.0 in 50 mM Tris-HCl buffer by the addition of Mn2+ at 0.05 mM, respectively Myxococcus xanthus
3.1.4.53 Co2+ the 3',5'-phosphodiesterase enzyme activities of PdeA and PdeB are stimulated 3.2fold and 1.98old, respectively, by 0.05 mM Co2+ at pH 8.0 in 50 mM Tris-HCl buffer Myxococcus xanthus
3.1.4.53 Mn2+ the 3',5'-phosphodiesterase enzyme activities of PdeA and PdeB are stimulated 4fold and 2.14old, respectively, by 0.05 mM Mn2+ at pH 8.0 in 50 mM Tris-HCl buffer Myxococcus xanthus
3.1.4.53 additional information the 3',5'-phosphodiesterase enzyme activities of PdeA and PdeB are not stimulated by 0.05 mM Ca2+, Mg2+, Fe2+, and Fe3+ Myxococcus xanthus

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.1.4.16 34000
-
 SDS-PAGE Myxococcus xanthus
3.1.4.17 29000
-
 PdeA, SDS-PAGE Myxococcus xanthus
3.1.4.17 34000
-
 PdeB, SDS-PAGE Myxococcus xanthus
3.1.4.53 29000
-
 PdeA, SDS-PAGE Myxococcus xanthus
3.1.4.53 29000
-
 PdeA, calculated from amino acid sequence Myxococcus xanthus
3.1.4.53 31000
-
 PdeB, calculated from amino acid sequence Myxococcus xanthus
3.1.4.53 34000
-
 PdeB, SDS-PAGE Myxococcus xanthus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.1.4.53 3',5'-cAMP + H2O Myxococcus xanthus
-
 5'-AMP the reaction product, 5'-AMP, is further dephosphorylated to adenosine by PdeA and PdeB ?
3.1.4.53 additional information Myxococcus xanthus Myxococcus xanthus PdeA and PdeB, enzymes hydrolyze 3',5'- and 2',3'-cyclic AMP to adenosine, and also demonstrate phosphatase activity toward nucleoside 5'-tri-, 5'-di-, 5'- and 3'-monophosphates with highest activities for nucleoside 5'-monophosphates. PdeA and PdeB also show high phosphomonoesterase activities against 50-UMP, 3'-AMP, and 3'-GMP, low activities against 5'-dAMP, and no activities toward 2'-AMP and 2'-GMP ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.1.4.16 Myxococcus xanthus
-
-
-
3.1.4.17 Myxococcus xanthus
-
-
-
3.1.4.53 Myxococcus xanthus
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.1.4.16 Talon affinity column chromatography Myxococcus xanthus
3.1.4.17 Talon column chromatography Myxococcus xanthus
3.1.4.53 Talon CellThru column chromatography, gel filtration Myxococcus xanthus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.4.16 cyclic 2',3'-AMP + H2O
-
 Myxococcus xanthus 3'-AMP
-
 r
3.1.4.16 additional information PdeB also shows high phosphomonoesterase activity against 5'-UMP, 3'-AMP, 3'-GMP, and low activity against 5'-dAMP Myxococcus xanthus ?
-
 ?
3.1.4.16 additional information the enzyme shows no activity toward 2'-AMP and 2'-GMP, 3',5'-cGMP is either not hydrolysed or is cleaved very slowly by PdeB Myxococcus xanthus ?
-
 ?
3.1.4.17 2',3'-cAMP + H2O in PdeB the phosphodiesterase activity for 2',3'-cAMP is about 1.7fold higher than that for 3',5'-cAMP Myxococcus xanthus 3'-AMP
-
 ?
3.1.4.17 3',5'-cAMP + H2O 3',5'-cAMP is completely hydrolyzed to adenosine when incubated with PdeA for a prolonged time Myxococcus xanthus 5'-AMP
-
 ?
3.1.4.17 3'-AMP + H2O high activity Myxococcus xanthus ?
-
 ?
3.1.4.17 3'-GMP + H2O high activity Myxococcus xanthus ?
-
 ?
3.1.4.17 5'-ATP + H2O
-
 Myxococcus xanthus ?
-
 ?
3.1.4.17 5'-dAMP + H2O low activity Myxococcus xanthus ?
-
 ?
3.1.4.17 5'-UMP + H2O high activity Myxococcus xanthus ?
-
 ?
3.1.4.17 additional information 3',5'-cGMP is either not hydrolysed or is cleaved very slowly by PdeA and PdeB, PdeA and PdeB show no activities toward 2'-AMP and 2'-GMP Myxococcus xanthus ?
-
 ?
3.1.4.17 additional information PdeA and PdeB hydrolyze 3',5'- and 2',3'-cyclic AMP to adenosine, and also demonstrate phosphatase activity toward nucleoside 5'-tri-, 5'-di-, 5'- and 3'-monophosphates with highest activities for nucleoside 5'-monophosphates Myxococcus xanthus ?
-
 ?
3.1.4.17 UDP-D-glucose + H2O UDP-D-glucose is hydrolyzed by PdeB, but not by PdeA Myxococcus xanthus ?
-
 ?
3.1.4.53 3',5'-cAMP + H2O
-
 Myxococcus xanthus 5'-AMP the reaction product, 5'-AMP, is further dephosphorylated to adenosine by PdeA and PdeB ?
3.1.4.53 additional information Myxococcus xanthus PdeA and PdeB, enzymes hydrolyze 3',5'- and 2',3'-cyclic AMP to adenosine, and also demonstrate phosphatase activity toward nucleoside 5'-tri-, 5'-di-, 5'- and 3'-monophosphates with highest activities for nucleoside 5'-monophosphates. PdeA and PdeB also show high phosphomonoesterase activities against 50-UMP, 3'-AMP, and 3'-GMP, low activities against 5'-dAMP, and no activities toward 2'-AMP and 2'-GMP Myxococcus xanthus ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.1.4.16 2',3'-cAMP phosphodiesterase
-
 Myxococcus xanthus
3.1.4.16 PdeB
-
 Myxococcus xanthus
3.1.4.17 PdeA has 3',5'- and 2',3'-cAMP phosphodiesterase and phosphomonoesterase activities Myxococcus xanthus
3.1.4.17 PdeB has 3',5'- and 2',3'-cAMP phosphodiesterase and phosphomonoesterase activities Myxococcus xanthus
3.1.4.53 PdeA
-
 Myxococcus xanthus
3.1.4.53 PdeB
-
 Myxococcus xanthus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.1.4.16 50
-
-
 Myxococcus xanthus
3.1.4.17 40
-
 the optimum temperature for the 3',5'-cAMP phosphodiesterase activity of PdeA is 40°C Myxococcus xanthus
3.1.4.17 50
-
 the optimum temperature for the 3',5'-cAMP phosphodiesterase activity of PdeA is 50°C Myxococcus xanthus
3.1.4.53 40
-
 the optimum temperatures for the 3',5'-cAMP phosphodiesterase activity of PdeA is 40°C Myxococcus xanthus
3.1.4.53 50
-
 the optimum temperatures for the 3',5'-cAMP phosphodiesterase activity of PdeB is 50°C Myxococcus xanthus

Temperature Range [°C]

EC Number Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
3.1.4.16 50 55 heat treatment at 50 or 55°C for 5 min slightly activates the phosphodiesterase activity of PdeB against 3',5'-cAMP by about 1.2fold Myxococcus xanthus
3.1.4.17 20 55
-
 Myxococcus xanthus

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.1.4.53 50 55 heat treatment at 50°C or 55°C for 5 min slightly activates the phosphodiesterase activity of PdeB against 3',5'-cAMP by about 1.2fold of the control while PdeA activity is not activated by the heat treatment Myxococcus xanthus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.4.16 0.0006
-
 cyclic 2',3'-AMP in 50 mM Tris-HCl, pH 8.0 Myxococcus xanthus
3.1.4.17 0.0006
-
 2',3'-cAMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.00093
-
 3',5'-cAMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.00096
-
 2',3'-cAMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.00096
-
 3',5'-cAMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.00155
-
 5'-ATP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.0031
-
 5'-AMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.00454
-
 5'-ATP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.17 0.00551
-
 5'-AMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.53 0.00093
-
 3',5'-cAMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.53 0.00096
-
 3',5'-cAMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.1.4.16 7.5 8.5 PdeB has slightly alkaline pH optimum (pH 7.5-8.5) for 3',5'-cAMP with 0.1 M Tris-HCl buffer Myxococcus xanthus
3.1.4.17 7.5 8.5 for 3',5'-cAMP with 0.1 M Tris-HCl buffer Myxococcus xanthus
3.1.4.53 7.5 8.5 PdeA and PdeB have slightly alkaline pH optima (pH 7.5-8.5) for 3',5'-cAMP hydrolysis in 0.1 M Tris-HCl buffer Myxococcus xanthus

pH Range

EC Number pH Minimum pH Maximum Comment Organism
3.1.4.17 5 9 PdeB shows no 3',5'-cAMP phosphodiesterase activity at or below pH 6 Myxococcus xanthus

pH Stability

EC Number pH Stability pH Stability Maximum Comment Organism
3.1.4.53 6 7 PdeB shows no 3',5'-cAMP phosphodiesterase activity at or below pH 6.0, PdeA and PdeB activities are strongly inhibited by 0.1 M sodium phosphate buffer (pH 6.0 and 7.0) Myxococcus xanthus

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.1.4.53 0.19
-
 3',5'-cAMP PdeB, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus
3.1.4.53 0.29
-
 3',5'-cAMP PdeA, in 50 mM Tris-HCl, pH 8.0, 0.05 mM MnCl2, at 40°C Myxococcus xanthus