Continued from EC 3.1.3.51 to EC 3.1.3.112
Accepted name: phosphodiesterase I
Reaction: Hydrolytically removes 5'-nucleotides successively from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides
Other name(s): 5'-exonuclease; 5'-phosphodiesterase; 5'-nucleotide phosphodiesterase
Systematic name: oligonucleotide 5'-nucleotidohydrolase
Comments: Low activity towards polynucleotides. A 3'-phosphate terminus on the substrate inhibits hydrolysis.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9025-82-5
References:
1. Khorana, G.H. Phosphodiesterases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds.), The Enzymes, 2nd edn., vol. 5, Academic Press, New York, 1961, pp. 79-94.
Accepted name: glycerophosphocholine phosphodiesterase
Reaction: sn-glycero-3-phosphocholine + H2O = choline + sn-glycerol 3-phosphate
Other name(s): glycerophosphinicocholine diesterase; glycerylphosphorylcholinediesterase; sn-glycero-3-phosphorylcholine diesterase; glycerolphosphorylcholine phosphodiesterase; glycerophosphohydrolase
Systematic name: sn-glycero-3-phosphocholine glycerophosphohydrolase
Comments: Also acts on sn-glycero-3-phosphoethanolamine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9025-85-8
References:
1. Dawson, R.M.C. Liver glycerylphosphorylcholine diesterase. Biochem. J. 62 (1956) 689-693.
2. Hayaishi, O. and Kornberg, A. Metabolism of phospholipides by bacterial enzymes. J. Biol. Chem. 206 (1954) 647-663.
3. Webster, G.R., Marples, E.A. and Thompson, R.H.S. Glycerylphosphorylcholine diesterase activity in nervous tissue. Biochem. J. 65 (1957) 374-377.
Accepted name: phospholipase C
Reaction: A phosphatidylcholine + H2O = 1,2-sn-diacylglycerol + phosphocholine
Other name(s): lipophosphodiesterase I; lecithinase C; Clostridium welchii α-toxin; Clostridium oedematiens β- and γ-toxins; lipophosphodiesterase C; phosphatidase C; heat-labile hemolysin; α-toxin
Systematic name: phosphatidylcholine cholinephosphohydrolase
Comments: The bacterial enzyme, which is a zinc protein, also acts on sphingomyelin and phosphatidylinositol; that from seminal plasma does not act on phosphatidylinositol.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9001-86-9
References:
1. Druzhinina, K.V. and Kritzman, M.G. [Lecithinase from animal tissues.] Biokhimiya 17 (1952) 77-81. (in Russian)
2. Little, C. and Otnass, A.-B. The metal ion dependence of phospholipase C from Bacillus cereus. Biochim. Biophys. Acta 391 (1975) 326-333. [PMID: 807246]
3. Sheiknejad, R.G. and Srivastava, P.N. Isolation and properties of a phosphatidylcholine-specific phospholipase C from bull seminal plasma. J. Biol. Chem. 261 (1986) 7544-7549. [PMID: 3086312]
4. Takahashi, T., Sugahara, T. and Ohsaka, A. Purification of Clostridium perfringens phospholipase C (α-toxin) by affinity chromatography on agarose-linked egg-yolk lipoprotein. Biochim. Biophys. Acta 351 (1974) 155-171. [PMID: 4365891]
Accepted name: phospholipase D
Reaction: A phosphatidylcholine + H2O = choline + a phosphatidate
Other name(s): lipophosphodiesterase II; lecithinase D; choline phosphatase
Systematic name: phosphatidylcholine phosphatidohydrolase
Comments: Also acts on other phosphatidyl esters.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9001-87-0
References:
1. Astrachan, L. The bond hydrolyzed by cardiolipin-specific phospholipase D. Biochim. Biophys. Acta 296 (1973) 79-88. [PMID: 4632675]
2. Einset, E. and Clark, W.L. The enzymatically catalyzed release of choline from lecithin. J. Biol. Chem. 231 (1958) 703-715.
3. Hanahan, D.J. and Chaikoff, I.L. On the nature of the phosphorus-containing lipides of cabbage leaves and their relation to a phospholipide-splitting enzyme contained in these leaves. J. Biol. Chem. 172 (1948) 191-198.
4. Tookey, H.L. and Balls, A.K. Plant phospholipase D. I. Studies on cottonseed and cabbage phospholipase D. J. Biol. Chem. 218 (1956) 213-224.
[3.1.4.5 Transferred entry: now EC 3.1.21.1 deoxyribonuclease I (EC 3.1.4.5 created 1961, deleted 1978)]
[3.1.4.6 Transferred entry: now EC 3.1.22.1 deoxyribonuclease II (EC 3.1.4.6 created 1961, deleted 1978)]
[3.1.4.7 Transferred entry: now EC 3.1.31.1 micrococcal nuclease (EC 3.1.4.7 created 1961, deleted 1978)]
[3.1.4.8 Transferred entry: now EC 3.1.27.3 ribonuclease T1 (EC 3.1.4.8 created 1961, transferred 1965 to EC 2.7.7.26, reinstated 1972, deleted 1978)]
[3.1.4.9 Transferred entry: now EC 3.1.30.2 Serratia marcescens nuclease (EC 3.1.4.9 created 1965, deleted 1978)]
[EC 3.1.4.10 Transferred entry: now EC 4.6.1.13, phosphatidylinositol diacylglycerol-lyase. As there is no hydrolysis of the inositol 1,2-cyclic phosphate formed, previous classification of the enzyme as a hydrolase was incorrect. (EC 3.1.4.10 created 1972, modified 1976, deleted 2002)]
Accepted name: phosphoinositide phospholipase C
Reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1D-myo-inositol 1,4,5-trisphosphate + diacylglycerol
For diagram click here.
Other name(s): triphosphoinositide phosphodiesterase; phosphoinositidase C; 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase; monophosphatidylinositol phosphodiesterase; phosphatidylinositol phospholipase C; PI-PLC; 1-phosphatidyl-D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase
Systematic name: 1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase
Comments: These enzymes form some of the cyclic phosphate Ins(cyclic1,2)P(4,5)P2 as well as Ins(1,4,5)P3. They show activity towards phosphatidylinositol, i.e., the activity of EC 4.6.1.13, phosphatidylinositol diacylglycerol-lyase, in vitro at high [Ca2+]. Four β-isoforms regulated by G-proteins, two γ-forms regulated by tyrosine kinases, four δ-forms regulated at least in part by calcium and an ε-form, probably regulated by the oncogene ras, have been found.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 63551-76-8
References:
1. Downes, C.P. and Michell, R.H. The polyphosphoinositide phosphodiesterase of erythrocyte membranes. Biochem. J. 198 (1981) 133-140. [PMID: 6275838]
2. Thompson, W. and Dawson, R.M.C. The triphosphoinositide phosphodiesterase of brain tissue. Biochem. J. 91 (1964) 237-243.
3. Rhee, S.G. and Bae, Y.S. Regulation of phosphoinositide-specific phospholipase C isozymes. J. Biol. Chem. 272 (1997) 15045-15048. [PMID: 9182519]
Accepted name: sphingomyelin phosphodiesterase
Reaction: a sphingomyelin + H2O = an N-acylsphingosine + phosphocholine
Other name(s): neutral sphingomyelinase
Systematic name: sphingomyelin cholinephosphohydrolase
Comments: Has very little activity on phosphatidylcholine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-54-3
References:
1. Barnholz, Y., Roitman, A. and Gatt, S. Enzymatic hydrolysis of sphingolipids. II. Hydrolysis of sphingomyelin by an enzyme from rat brain. J. Biol. Chem. 241 (1966) 3731-3737. [PMID: 5916388]
2. Chatterjee, S. and Ghosh, N. Neutral sphingomyelinase from human urine. Purification and preparation of monospecific antibodies. J. Biol. Chem. 264 (1989) 12554-12561. [PMID: 2545711]
3. Heller, M. and Shapiro, B. Enzymic hydrolysis of sphingomyelin by rat liver. Biochem. J. 98 (1966) 763-769. [PMID: 5911524]
4. Kanfer, J.N., Young, O.M., Shapiro, D. and Brady, R.O. The metabolism of sphingomyelin. I. Purification and properties of a sphingomyelin-cleaving enzyme from rat liver tissue. J. Biol. Chem. 241 (1966) 1081-1084. [PMID: 5933867]
Accepted name: serine-ethanolaminephosphate phosphodiesterase
Reaction: serine phosphoethanolamine + H2O = serine + ethanolamine phosphate
Other name(s): serine ethanolamine phosphodiester phosphodiesterase; SEP diesterase
Systematic name: serine-phosphoethanolamine ethanolaminephosphohydrolase
Comments: Acts only on those phosphodiesters that have ethanolamine as a component part of the molecule.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37288-20-3
References:
1. Hagerman, D.D., Rosenberg, H., Ennor, A.H., Schiff, P. and Inove, S. The isolation and properties of chicken kidney serine ethanolamine phosphate phosphodiesterase. J. Biol. Chem. 240 (1965) 1108-1012.
Accepted name: [acyl-carrier-protein] phosphodiesterase
Reaction: holo-[acyl-carrier protein] + H2O = 4'-phosphopantetheine + apo-[acyl-carrier protein]
Other name(s): ACP hydrolyase; ACP phosphodiesterase; AcpH; [acyl-carrier-protein] 4'-pantetheine-phosphohydrolase
Systematic name: holo-[acyl-carrier protein] 4'-pantetheine-phosphohydrolase
Comments: The enzyme cleaves acyl-[acyl-carrier protein] species with acyl chains of 6-16 carbon atoms although it appears to demonstrate a preference for the unacylated acyl-carrier-protein (ACP) and short-chain ACPs over the medium- and long-chain species [3]. Deletion of the gene encoding this enzyme abolishes ACP prosthetic-group turnover in vivo [3]. Activation of apo-ACP to form the holoenzyme is carried out by EC 2.7.8.7, holo-[acyl-carrier-protein] synthase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37288-21-4
References:
1. Sobhy, C. Regulation of fatty acid synthetase activity. The 4'-phosphopantetheine hydrolase of rat liver. J. Biol. Chem. 254 (1979) 8561-8566. [PMID: 224058]
2. Vagelos, P.R. and Larrabee, A.R. Acyl carrier protein. IX. Acyl carrier protein hydrolase. J. Biol. Chem. 242 (1967) 1776-1781. [PMID: 4290442]
3. Thomas, J. and Cronan, J.E. The enigmatic acyl carrier protein phosphodiesterase of Escherichia coli: genetic and enzymological characterization. J. Biol. Chem. 280 (2005) 34675-34683. [PMID: 16107329]
[EC 3.1.4.15 Transferred entry: adenylyl-[glutamateammonia ligase] hydrolase. As it has been shown that the enzyme catalyses a transfer of the adenylyl group to phosphate, the enzyme has been transferred to EC 2.7.7.89, adenylyl-[glutamateammonia ligase] phosphorylase (EC 3.1.4.15 created 1972, deleted 2015)]
Accepted name: 2',3'-cyclic-nucleotide 2'-phosphodiesterase
Reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate
Other name(s): ribonucleoside 2',3'-cyclic phosphate diesterase; 2',3 '-cyclic AMP phosphodiesterase; 2',3'-cyclic nucleotidase; cyclic 2',3'-nucleotide 2'-phosphodiesterase; cyclic 2',3'-nucleotide phosphodiesterase; 2',3'-cyclic nucleoside monophosphate phosphodiesterase; 2',3'-cyclic AMP 2'-phosphohydrolase; cyclic phosphodiesterase:3'-nucleotidase; 2',3'-cyclic nucleotide phosphohydrolase; 2':3'-cyclic phosphodiesterase; 2':3'-cyclic nucleotide phosphodiesterase:3'-nucleotidase
Systematic name: nucleoside-2',3'-cyclic-phosphate 3'-nucleotidohydrolase
Comments: Also hydrolyses 3'-nucleoside monophosphates and bis-4-nitrophenyl phosphate, but not 3'-deoxynucleotides. Similar reactions are carried out by EC 4.6.1.24 (ribonuclease T1) and EC 4.6.1.18 (pancreatic ribonuclease).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9037-18-7
References:
1. Anraku, Y. A new cyclic phosphodiesterase having a 3'-nucleotidase activity from Escherichia coli B. I. Purification and some properties of the enzyme. J. Biol. Chem. 239 (1964) 3412-3419.
2. Anraku, Y. A new cyclic phosphodiesterase having a 3'-nucleotidase activity from Escherichia coli B. II. Further studies on substrate specificity and mode of action of the enzyme. J. Biol. Chem. 239 (1964) 3420-3424.
3. Center, M.S. and Behal, F.J. A cyclic phosphodiesterase with 3'-nucleotidase activity from Proteus mirabilis. J. Biol. Chem. 243 (1968) 138-143. [PMID: 4295113]
4. Olafson, R.W., Drummond, G.I. and Lee, J.F. Studies on 2',3'-cyclic nucleotide-3'-phosphohydrolase from brain. Can. J. Biochem. 47 (1969) 961-966. [PMID: 4310670]
5. Unemoto, T. and Hayashi, M. Chloride ion as a modifier of 2',3'-cyclic phosphodiesterase purified from halophilic Vibrio alginolyticus. Biochim. Biophys. Acta 171 (1969) 89-102. [PMID: 4303200]
Accepted name: 3',5'-cyclic-nucleotide phosphodiesterase
Reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate
Other name(s): cyclic 3',5'-mononucleotide phosphodiesterase; PDE; cyclic 3',5'-nucleotide phosphodiesterase; cyclic 3',5'-phosphodiesterase; 3',5'-nucleotide phosphodiesterase; 3':5'-cyclic nucleotide 5'-nucleotidohydrolase; 3',5'-cyclonucleotide phosphodiesterase; cyclic nucleotide phosphodiesterase; 3', 5'-cyclic nucleoside monophosphate phosphodiesterase; 3': 5'-monophosphate phosphodiesterase (cyclic CMP); cytidine 3':5'-monophosphate phosphodiesterase (cyclic CMP); cyclic 3',5-nucleotide monophosphate phosphodiesterase; nucleoside 3',5'-cyclic phosphate diesterase; nucleoside-3',5-monophosphate phosphodiesterase
Systematic name: 3',5'-cyclic-nucleotide 5'-nucleotidohydrolase
Comments: Acts on 3',5'-cyclic AMP, 3',5'-cyclic dAMP, 3',5'-cyclic IMP, 3',5'-cyclic GMP and 3',5'-cyclic CMP.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9040-59-9
References:
1. Fischer, U. and Amrhein, N. Cyclic nucleotide phosphodiesterase of Chlamydomonas reinhardtii. Biochim. Biophys. Acta 341 (1974) 412-420. [PMID: 4365506]
2. Nair, K.G. Purification and properties of 3',5'-cyclic nucleotide phosphodiesterase from dog heart. Biochemistry 5 (1966) 150-157. [PMID: 4287216]
[EC 3.1.4.18 Transferred entry: now EC 3.1.16.1 spleen exonuclease (EC 3.1.4.18 created 1972, deleted 1978)]
[EC 3.1.4.19 Transferred entry: now EC 3.1.13.3 oligonucleotidase (EC 3.1.4.19 created 1972, deleted 1978)]
[EC 3.1.4.20 Transferred entry: now EC 3.1.13.1 exoribonuclease II (EC 3.1.4.20 created 1972, deleted 1978)]
[EC 3.1.4.21 Transferred entry: now EC 3.1.30.1 Aspergillus nuclease S1 (EC 3.1.4.21 created 1972, deleted 1978)]
[EC 3.1.4.22 Transferred entry: now EC 3.1.27.5 pancreatic ribonuclease (EC 3.1.4.22 created 1972, deleted 1978)]
[EC 3.1.4.23 Transferred entry: now EC 3.1.27.1 ribonculease T2 (EC 3.1.4.23 created 1972, deleted 1978)]
[EC 3.1.4.24 Deleted entry: endoribonuclease III (EC 3.1.4.24 created 1972, deleted 1978)]
[EC 3.1.4.25 Transferred entry: now EC 3.1.11.1 exodeoxyribonuclease I (EC 3.1.4.25 created 1972, deleted 1978)]
[EC 3.1.4.26 Deleted entry: exodeoxyribonuclease II (EC 3.1.4.26 created 1972, deleted 1978)]
[EC 3.1.4.27 Transferred entry: now EC 3.1.11.2 exodeoxyribonuclease III (EC 3.1.4.27 created 1972, deleted 1978)]
[EC 3.1.4.28 Transferred entry: now EC 3.1.11.3 exodeoxyribonuclease (lambda-induced) (EC 3.1.4.28 created 1972, deleted 1978)]
[EC 3.1.4.29 Deleted entry: oligodeoxyribonucleate exonuclease (EC 3.1.4.29 created 1972, deleted 1978)]
[EC 3.1.4.30 Transferred entry: now EC 3.1.21.2 deoxyribonuclease IV (phage T4-induced) (EC 3.1.4.30 created 1972, deleted 1978)]
[EC 3.1.4.31 Transferred entry: now EC 3.1.11.4 exodeoxyribonuclease (phage SP3-induced) (EC 3.1.4.31 created 1972, deleted 1978)]
[EC 3.1.4.32 Deleted entry: endodeoxyribonuclease (ATP- and S-adenosylmethionine-dependent). See EC 3.1.21.3 type 1 site-specific deoxyribonuclease and EC 3.1.21.5 type III site-specific deoxyribonuclease (EC 3.1.4.32 created 1972, deleted 1978)]
[EC 3.1.4.33 Deleted entry: endodeoxyribonuclease (ATP-hydrolysing). See EC 3.1.21.3 type 1 site-specific deoxyribonuclease and EC 3.1.21.5 type III site-specific deoxyribonuclease (EC 3.1.4.33 created 1972, deleted 1978)]
[EC 3.1.4.34 Deleted entry: hybrid nuclease. See subclasses EC 3.1.15, EC 3.1.16, EC 3.1.30 and EC 3.1.31 (EC 3.1.4.34 created 1972, deleted 1978)]
Accepted name: 3',5'-cyclic-GMP phosphodiesterase
Reaction: guanosine 3',5'-cyclic phosphate + H2O = GMP
Glossary: GMP = guanosine 5'-phosphate
Other name(s): guanosine cyclic 3',5'-phosphate phosphodiesterase; cyclic GMP phosphodiesterase; cyclic 3',5'-GMP phosphodiesterase; cyclic guanosine 3',5'-monophosphate phosphodiesterase; cyclic guanosine 3',5'-phosphate phosphodiesterase; cGMP phosphodiesterase; cGMP-PDE; cyclic guanosine 3',5'-phosphate phosphodiesterase
Systematic name: 3',5'-cyclic-GMP 5'-nucleotidohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9068-52-4
References:
1. Marks, F. and Raab, I. The second messenger system of mouse epidermis. IV. Cyclic AMP and cyclic GMP phosphodiesterase.Biochim. Biophys. Acta 334 (1974) 368-377.
[EC 3.1.4.36 Deleted entry: 1,2-cyclic-inositol-phosphate phosphodiesterase. Now included with EC 3.1.4.43, glycerophosphoinositol inositolphosphodiesterase (EC 3.1.4.36 created 1976, deleted 2002)]
Accepted name: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate
Other name(s): cyclic-CMP phosphodiesterase; 2',3'-cyclic AMP phosphodiesterase; cyclic 2',3'-nucleotide 3'-phosphodiesterase; cyclic 2',3'-nucleotide phosphodiesterase; 2',3'-cyclic nucleoside monophosphate phosphodiesterase; 2',3'-cyclic nucleotide 3'-phosphohydrolase; CNPase; 2',3'-cyclic nucleotide phosphohydrolase; 2':3'-cyclic nucleotide 3'-phosphodiesterase; 2':3'-CNMP-3'-ase
Systematic name: nucleoside-2',3'-cyclic-phosphate 2'-nucleotidohydrolase
Comments: The brain enzyme acts on 2',3'-cyclic AMP more rapidly than on the UMP or CMP derivatives. An enzyme from liver acts on 2',3'-cyclic CMP more rapidly than on the purine derivatives; it also hydrolyses the corresponding 3',5'-cyclic phosphates, but more slowly. This latter enzyme has been called cyclic-CMP phosphodiesterase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 60098-35-3
References:
1. Drummond, G.I., Iyer, N.T. and Keith, J. Hydrolysis of ribonucleoside 2',3'-cyclic phosphates by a diesterase from brain. J. Biol. Chem. 237 (1962) 3535-3539.
2. Helfman, D.M. and Kuo, J.F. A homogeneous cyclic CMP phosphodiesterase hydrolyzes both pyrimidine and purine cyclic 2':3'- and 3':5'-nucleotides. J. Biol. Chem. 257 (1982) 1044-1047. [PMID: 6274851]
3. Helfman, D.M., Shoji, M. and Kuo, J.F. Purification to homogeneity and general properties of a novel phosphodiesterase hydrolyzing cyclic CMP and cyclic AMP. J. Biol. Chem. 256 (1981) 6327-6334. [PMID: 6263914]
4. Kurihara, T., Nishizawa, Y., Takahashi, Y. and Odani, S. Chemical, immunological and catalytic properties of 2':3'-cyclic nucleotide 3'-phosphodiesterase purified from brain white matter. Biochem. J. 195 (1981) 153-157. [PMID: 6272743]
5. Nishizawa, Y., Kurihara, T. and Takahashi, Y. Spectrophotometric assay, solubilization and purification of brain 2':3'-cyclic nucleotide 3'-phosphodiesterase. Biochem. J. 191 (1980) 71-82. [PMID: 6258586]
Accepted name: glycerophosphocholine cholinephosphodiesterase
Reaction: sn-glycero-3-phosphocholine + H2O = glycerol + phosphocholine
Other name(s): L-3-glycerylphosphinicocholine cholinephosphohydrolase
Systematic name: sn-glycero-3-phosphocholine cholinephosphohydrolase
Comments: No activity on sn-3-glycerophosphoethanolamine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 60063-78-7
References:
1. Abra, R.M. and Quinn, P.J. A novel pathway for phosphatidylcholine catabolism in rat brain homogenates. Biochim. Biophys. Acta 380 (1975) 436-441. [PMID: 166661]
Accepted name: alkylglycerophosphoethanolamine phosphodiesterase
Reaction: 1-alkyl-sn-glycero-3-phosphoethanolamine + H2O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine
Other name(s): lysophospholipase D
Systematic name: 1-alkyl-sn-glycero-3-phosphoethanolamine ethanolaminehydrolase
Comments: Also acts on acyl and choline analogues.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 62213-15-4
References:
1. Wykle, R.L. and Schremmer, J.M. A lysophospholipase D pathway in the metabolism of ether-linked lipids in brain microsomes. J. Biol. Chem. 249 (1974) 1742-1746. [PMID: 4855486]
Accepted name: CMP-N-acylneuraminate phosphodiesterase
Reaction: CMP-N-acylneuraminate + H2O = CMP + N-acylneuraminate
Other name(s): CMP-sialate hydrolase; CMP-sialic acid hydrolase; CMP-N-acylneuraminic acid hydrolase; cytidine monophosphosialic hydrolase; cytidine monophosphosialate hydrolase; cytidine monophosphate-N-acetylneuraminic acid hydrolase; CMP-N-acetylneuraminate hydrolase
Systematic name: CMP-N-acylneuraminate N-acylneuraminohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 55326-41-5
References:
1. Kean, E.L. and Bighouse, K.J. Cytidine 5'-monophosphosialic acid hydrolase. Subcellular location and properties. J. Biol. Chem. 249 (1974) 7813-7823. [PMID: 4372219]
Accepted name: sphingomyelin phosphodiesterase D
Reaction: sphingomyelin + H2O = ceramide phosphate + choline
Other name(s): sphingomyelinase D
Systematic name: sphingomyelin ceramide-phosphohydrolase
Comments: Does not act on phosphatidylcholine, but hydrolyses 2-lysophosphatidylcholine to choline and 2-lysophosphatidate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 54992-31-3
References:
1. Carne, H.R. and Onon, E. Action of Corynebacterium ovis exotoxin on endothelial cells of blood vessels. Nature 271 (1978) 246-248. [PMID: 622164]
2. Soucek, A., Michalec, C. and Souckov, A. Identification and characterization of a new enzyme of the group phospholipase D isolated from Corynebacterium ovis. Biochim. Biophys. Acta 227 (1971) 116-128. [PMID: 5543581]
Accepted name: glycerol-1,2-cyclic-phosphate 2-phosphodiesterase
Reaction: glycerol 1,2-cyclic phosphate + H2O = glycerol 1-phosphate
Other name(s): rac-glycerol 1:2-cyclic phosphate 2-phosphodiesterase
Systematic name: rac-glycerol-1,2-cyclic-phosphate 2-glycerophosphohydrolase
Comments: Acts on both stereoisomers of the substrate and also, more slowly, on 3',5'-cyclic AMP and on 2',3'-cyclic AMP.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 69458-89-5
References:
1. Clarke, N. and Dawson, R.M.C. rac-Glycerol 1:2-cyclic phosphate 2-phosphodiesterase, a new soluble phosphodiesterase of mammalian tissues. Biochem. J. 173 (1978) 579-589. [PMID: 212014]
Accepted name: glycerophosphoinositol inositolphosphodiesterase
Reaction: 1-(sn-glycero-3-phospho)-1D-myo-inositol + H2O = glycerol + 1D-myo-inositol 1-phosphate
For diagram click here.
Other name(s): 1,2-cyclic-inositol-phosphate phosphodiesterase; D-myo-inositol 1:2-cyclic phosphate 2-phosphohydrolase; D-inositol 1,2-cyclic phosphate 2-phosphohydrolase; D-myo-inositol 1,2-cyclic phosphate 2-phosphohydrolase; 1-D-myo-inositol-1,2-cyclic-phosphate 2-inositolphosphohydrolase; inositol-1,2-cyclic-phosphate 2-inositolphosphohydrolase
Systematic name: 1-(sn-glycero-3-phospho)-1D-myo-inositol inositolphosphohydrolase
Comments: This enzyme also hydrolyses Ins(cyclic 1,2)P to Ins-1-P
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9076-91-9 (from EC 3.1.4.36), 72414-13-2 (not distinguished from EC 3.1.4.44)
References:
1. Dawson, R.M.C. and Hemington, N. A phosphodiesterase in rat kidney cortex that hydrolyses glycerylphosphorylinositol. Biochem. J. 162 (1977) 241-245. [PMID: 192216]
2. Dawson, R.M.C. and Clarke, N.G. D-myoInositol 1:2-cyclic phosphate 2-phosphohydrolase. Biochem. J. 127 (1972) 113-118. [PMID: 4342209]
3. Dawson, R.M.C. and Clarke, N.G. A comparison of D-inositol 1:2-cyclic phosphate 2-phosphohydrolase with other phosphodiesterases of kidney. Biochem. J. 134 (1973) 59-67. [PMID: 4353088]
4. Ross, T.S. and Majerus, P.W. Inositol-1,2-cyclic-phosphate 2-inositolphosphohydrolase. Substrate specificity and regulation of activity by phospholipids, metal ion chelators, and inositol 2-phosphate. J. Biol. Chem. 266 (1991) 851-856. [PMID: 1845995]
Accepted name: glycerophosphoinositol glycerophosphodiesterase
Reaction: 1-(sn-glycero-3-phospho)-1D-myo-inositol + H2O = myo-inositol + sn-glycerol 3-phosphate
For diagram click here.
Other name(s): sn-glycero(3)phosphoinositol glycerophosphohydrolase; sn-glycero-3-phospho-1-inositol glycerophosphohydrolase
Systematic name: 1-(sn-glycero-3-phospho)-1D-myo-inositol glycerophosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 72414-13-2 (not distinguished from EC 3.1.4.43)
References:
1. Dawson, R.M.C., Hemington, N., Richards, D.E. and Irvine, R.F. sn-Glycero(3)phosphoinositol glycerophosphohydrolase. A new phosphodiesterase in rat tissues. Biochem. J. 182 (1979) 39-49. [PMID: 40550]
Accepted name: N-acetylglucosamine-1-phosphodiester α-N-acetylglucosaminidase
Reaction: glycoprotein N-acetyl-D-glucosaminyl-phospho-D-mannose + H2O = N-acetyl-D-glucosamine + glycoprotein phospho-D-mannose
Other name(s): α-N-acetylglucosaminyl phosphodiesterase; lysosomal α-N-acetylglucosaminidase; phosphodiester glycosidase; α-N-acetyl-D-glucosamine-1-phosphodiester N-acetylglucosaminidase; 2-acetamido-2-deoxy-α-D-glucose 1-phosphodiester acetamidodeoxyglucohydrolase
Systematic name: glycoprotein-N-acetyl-D-glucosaminyl-phospho-D-mannose N-acetyl-D-glucosaminylphosphohydrolase
Comments: Acts on a variety of compounds in which N-acetyl-D-glucosamine is α-linked to a phosphate group, including the biosynthetic intermediates of the high mannose oligosaccharide components of some lysosomal enzymes and the products of EC 2.7.8.17 UDP-N-acetylglucosamine#151;lysosomal-enzyme N-acetylglucosaminephosphotransferase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 75788-84-0
References:
1. Van den Tweel, W.J.J., Smits, J.P., Ogg, R.L.H.P. and De Bont, J.A.M. The involvement of an enantioselective transaminase in the metabolism of D-3- and D-4-hydroxyphenylglycine in Pseudomonas putida LW-4. Appl. Microbiol. Biotechnol. 29 (1988) 224-230.
2. van der Drift, C., van Helvoort, P.E.M. and Vogels, G.D. S-Ureidoglycolate dehydrogenase: purification and properties. Arch. Biochem. Biophys. 145 (1971) 465-469. [PMID: 4399430]
3. van der Drift, L., Vogels, G.D. and van der Drift, C. Allantoin racemase: a new enzyme from Pseudomonas species. Biochim. Biophys. Acta 391 (1975) 240-248. [PMID: 237557]
4. Waheed, A., Hasilik, A. and von Figura, K. Processing of the phosphorylated recognition marker in lysosomal enzymes. Characterization and partial purification of a microsomal α-N-acetylglucosaminyl phosphodiesterase. J. Biol. Chem. 256 (1981) 5717-5721. [PMID: 6263889]
Accepted name: glycerophosphodiester phosphodiesterase
Reaction: A glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate
Other name(s): gene hpd protein; glycerophosphoryl diester phosphodiesterase; IgD-binding protein D
Systematic name: glycerophosphodiester glycerophosphohydrolase
Comments: Broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol and bis(glycerophospho)-glycerol are hydrolysed.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 86280-59-3
References:
1. Larson, T.J., Ehrmann, M. and Boos, W. Periplasmic glycerophosphodiester phosphodiesterase of Escherichia coli, a new enzyme of the glp regulon. J. Biol. Chem. 258 (1983) 5428-5432. [PMID: 6304089]
[EC 3.1.4.47 Transferred entry: now EC 4.6.1.14, glycosylphosphatidylinositol diacylglycerol-lyase (EC 3.1.4.47 created 1989, deleted 2002)]
Accepted name: dolichylphosphate-glucose phosphodiesterase
Reaction: dolichyl β-D-glucosyl phosphate + H2O = dolichyl phosphate + D-glucose
Other name(s): dolichol phosphoglucose phosphodiesterase; Dol-P-Glc phosphodiesterase
Systematic name: dolichyl-β-D-glucosyl-phosphate dolichylphosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 89287-42-3
References:
1. Crean, E.V. Synthesis and degradation of dolichyl phosphoryl glucose by the cellular slime mold, Dictyostelium discoideum. Biochim. Biophys. Acta 792 (1984) 149-157.
Accepted name: dolichylphosphate-mannose phosphodiesterase
Reaction: dolichyl β-D-mannosyl phosphate + H2O = dolichyl phosphate + D-mannose
Other name(s): mannosylphosphodolichol phosphodiesterase
Systematic name: dolichyl-β-D-mannosyl-phosphate dolichylphosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 111839-07-7
References:
1. Tomita, Y. and Motokawa, Y. Characterization and partial purification of a novel mannosylphosphodolichol phosphodiesterase from chicken liver microsomes. Eur. J. Biochem. 170 (1987) 363-368. [PMID: 2826159]
Accepted name: glycosylphosphatidylinositol phospholipase D
Reaction: 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol + H2O = 6-(α-D-glucosaminyl)-1D-myo-inositol + 3-sn-phosphatidate
For diagram click here.
Other name(s): GPI-PLD; glycoprotein phospholipase D; phosphatidylinositol phospholipase D; phosphatidylinositol-specific phospholipase D
Systematic name: glycoprotein-phosphatidylinositol phosphatidohydrolase
Comments: This enzyme is also active when O-4 of the glucosamine is substituted by carrying the oligosaccharide that can link a protein to the structure. It therefore cleaves proteins from the lipid part of the glycosylphosphatidylinositol (GPI) anchors, but does so by hydrolysis, whereas glycosylphosphatidylinositol diacylglycerol-lyase (EC 4.6.1.14) does so by elimination. It acts on plasma membranes only after solubilization of the substrate with detergents or solvents, but it may act on intracellular membranes.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 113756-14-2
References:
1. Low, M.G. and Prasad, A.R.S. A phospholipase D specific for the phosphatidylinositol anchor of cell-surface proteins is abundant in plasma. Proc. Natl. Acad. Sci. USA 85 (1988) 980-984. [PMID: 3422494]
2. Malik, A.-S. and Low, M.G. Conversion of human placental alkaline phosphatase from a high Mr form to a low Mr form during butanol extraction. An investigation of the role of endogenous phosphoinositide-specific phospholipases. Biochem. J. 240 (1986) 519-527. [PMID: 3028377]
3. Li, J.Y., Hollfelder, K., Huang, K.S. and Low, M.G. Structural features of GPI-specific phospholipase D revealed by fragmentation and Ca2+ binding studies. J. Biol. Chem. 269 (1994) 28963-28971. [PMID: 7961859]
4. Deeg, M.A,, Vierman, E.L. and Cheung, M.C. GPI-specific phospholipase D associates with an apoA-I- and apoA-IV-containing complex. J. Lipid Res. 42 (2001) 442-451. [PMID: 11254757]
Accepted name: glucose-1-phospho-D-mannosylglycoprotein phosphodiesterase
Reaction: 6-(D-glucose-1-phospho)-D-mannosylglycoprotein + H2O = α-D-glucose 1-phosphate + D-mannosylglycoprotein
Other name(s): α-glucose-1-phosphate phosphodiesterase
Systematic name: 6-(D-glucose-1-phospho)-D-mannosylglycoprotein glucose-1-phosphohydrolase
Comments: The enzyme is specific for the product of EC 2.7.8.19 UDP-glucose—glycoprotein glucose phosphotransferase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 123940-44-3
References:
1. Srisomsap, C., Richardson, K.L., Jay, J.C. and Marchase, R.B. An α-glucose-1-phosphate phosphodiesterase is present in rat liver cytosol. J. Biol. Chem. 264 (1989) 20540-20546. [PMID: 2555363]
Accepted name: cyclic-guanylate-specific phosphodiesterase
Reaction: cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'→5')guanosine
For diagram of reaction click here
Glossary: c-di-GMP = c-di-guanylate = cyclic di-3',5'-guanylate = cyclic-bis(3'→5') dimeric GMP
Other name(s): cyclic bis(3→5')diguanylate phosphodiesterase; c-di-GMP-specific phosphodiesterase; c-di-GMP phosphodiesterase; phosphodiesterase; phosphodiesterase A1; PDEA1; VieA
Systematic name: cyclic bis(3→5')diguanylate 3'-guanylylhydrolase
Comments: Requires Mg2+ or Mn2+ for activity and is inhibited by Ca2+ and Zn2+. Contains a heme unit. This enzyme linearizes cyclic di-3',5'-guanylate, the product of EC 2.7.7.65, diguanylate cyclase and an allosteric activator of EC 2.4.1.12, cellulose synthase (UDP-forming), rendering it inactive [1]. It is the balance between these two enzymes that determines the cellular level of c-di-GMP [1].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Chang, A.L., Tuckerman, J.R., Gonzalez, G., Mayer, R., Weinhouse, H., Volman, G., Amikam, D., Benziman, M. and Gilles-Gonzalez, M.A. Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 40 (2001) 3420-3426. [PMID: 11297407]
2. Christen, M., Christen, B., Folcher, M., Schauerte, A. and Jenal, U. Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. J. Biol. Chem. 280 (2005) 30829-30837. [PMID: 15994307]
3. Schmidt, A.J., Ryjenkov, D.A. and Gomelsky, M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J. Bacteriol. 187 (2005) 4774-4781. [PMID: 15995192]
4. Tamayo, R., Tischler, A.D. and Camilli, A. The EAL domain protein VieA is a cyclic diguanylate phosphodiesterase. J. Biol. Chem. 280 (2005) 33324-33330. [PMID: 16081414]
Accepted name: 3',5'-cyclic-AMP phosphodiesterase
Reaction: adenosine 3',5'-cyclic phosphate + H2O = AMP
Glossary: AMP = adenosine 5'-phosphate
Other name(s): cAMP-specific phosphodiesterase; cAMP-specific PDE; PDE1; PDE2A; PDE2B; PDE4; PDE7; PDE8; PDEB1; PDEB2
Systematic name: 3',5'-cyclic-AMP 5'-nucleotidohydrolase
Comments: Requires Mg2+ or Mn2+ for activity [2]. This enzyme is specific for 3',5'-cAMP and does not hydrolyse other nucleoside 3',5'-cyclic phosphates such as cGMP (c.f. EC 3.1.4.17, 3"-cyclic-nucleotide phosphodiesterase and EC 3.1.4.35, 3',5'-cyclic-GMP phosphodiesterase). It is involved in modulation of the levels of cAMP, which is a mediator in the processes of cell transformation and proliferation [3].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Alonso, G.D., Schoijet, A.C., Torres, H.N. and Flawiá, M.M. TcPDE4, a novel membrane-associated cAMP-specific phosphodiesterase from Trypanosoma cruzi. Mol. Biochem. Parasitol. 145 (2006) 40-49. [PMID: 16225937]
2. Bader, S., Kortholt, A., Snippe, H. and Van Haastert, P.J. DdPDE4, a novel cAMP-specific phosphodiesterase at the surface of Dictyostelium cells. J. Biol. Chem. 281 (2006) 20018-20026. [PMID: 16644729]
3. Rascón, A., Soderling, S.H., Schaefer, J.B. and Beavo, J.A. Cloning and characterization of a cAMP-specific phosphodiesterase (TbPDE2B) from Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 99 (2002) 4714-4719. [PMID: 11930017]
4. Johner, A., Kunz, S., Linder, M., Shakur, Y. and Seebeck, T. Cyclic nucleotide specific phosphodiesterases of Leishmania major. BMC Microbiol. 6:25 (2006). [PMID: 16522215]
5. Lugnier, C., Keravis, T., Le Bec, A., Pauvert, O., Proteau, S. and Rousseau, E. Characterization of cyclic nucleotide phosphodiesterase isoforms associated to isolated cardiac nuclei. Biochim. Biophys. Acta 1472 (1999) 431-446. [PMID: 10564757]
6. Imamura, R., Yamanaka, K., Ogura, T., Hiraga, S., Fujita, N., Ishihama, A. and Niki, H. Identification of the cpdA gene encoding cyclic 3',5'-adenosine monophosphate phosphodiesterase in Escherichia coli. J. Biol. Chem. 271 (1996) 25423-25429. [PMID: 8810311]
Accepted name: N-acetylphosphatidylethanolamine-hydrolysing phospholipase D
Reaction: N-acylphosphatidylethanolamine + H2O = N-acylethanolamine + a 1,2-diacylglycerol 3-phosphate
Other name(s): NAPE-PLD; anandamide-generating phospholipase D; N-acyl phosphatidylethanolamine phospholipase D; NAPE-hydrolyzing phospholipase D
Systematic name: N-acetylphosphatidylethanolamine phosphatidohydrolase
Comments: This enzyme is involved in the biosynthesis of anandamide. It does not hydrolyse phosphatidylcholine and phosphatidylethanolamine [1]. No transphosphatidation [1]. The enzyme contains Zn2+ and is activated by Mg2+ or Ca2+ [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Okamoto, Y., Morishita, J., Tsuboi, K., Tonai, T. and Ueda, N. Molecular characterization of a phospholipase D generating anandamide and its congeners. J. Biol. Chem. 279 (2004) 5298-5305. [PMID: 14634025]
2. Wang, J., Okamoto, Y., Morishita, J., Tsuboi, K., Miyatake, A. and Ueda, N. Functional analysis of the purified anandamide-generating phospholipase D as a member of the metallo-β-lactamase family. J. Biol. Chem. 281 (2006) 12325-12335. [PMID: 16527816]
Accepted name: phosphoribosyl 1,2-cyclic phosphate phosphodiesterase
Reaction: 5-phospho-α-D-ribose 1,2-cyclic phosphate + H2O = α-D-ribose 1,5-bisphosphate
For diagram of reaction click here.
Other name(s): phnP (gene name)
Systematic name: 5-phospho-α-D-ribose 1,2-cyclic phosphate 2-phosphohydrolase (α-D-ribose 1,5-bisphosphate-forming)
Comments: Binds Mn2+ and Zn2+. Isolated from the bacterium Escherichia coli, where it participates in the degradation of methylphosphonate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Podzelinska, K., He, S.M., Wathier, M., Yakunin, A., Proudfoot, M., Hove-Jensen, B., Zechel, D.L. and Jia, Z. Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation. J. Biol. Chem. 284 (2009) 17216-17226. [PMID: 19366688]
2. Hove-Jensen, B., McSorley, F.R. and Zechel, D.L. Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway. J. Am. Chem. Soc. 133 (2011) 3617-3624. [PMID: 21341651]
3. He, S.M., Wathier, M., Podzelinska, K., Wong, M., McSorley, F.R., Asfaw, A., Hove-Jensen, B., Jia, Z. and Zechel, D.L. Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway. Biochemistry 50 (2011) 8603-8615. [PMID: 21830807]
Accepted name: 7,8-dihydroneopterin 2',3'-cyclic phosphate phosphodiesterase
Reaction: (1) 7,8-dihydroneopterin 2',3'-cyclic phosphate + H2O = 7,8-dihydroneopterin 3'-phosphate
(2) 7,8-dihydroneopterin 2',3'-cyclic phosphate + H2O = 7,8-dihydroneopterin 2'-phosphate
For diagram of reaction click here.
Glossary: 7,8-dihydroneopterin 2',3'-cyclic phosphate = 2-amino-6-{(S)-hydroxy[(4R)-2-hydroxy-2-oxido-1,3,2-dioxaphospholan-4-yl]methyl}-7,8-dihydropteridin-4(1H)-one = 2-amino-6-[(1S,2R)-1,2,3-trihydroxypropyl]-7,8-dihydro-4(1H)-pteridinone 1,2-cyclic phosphate
7,8-dihydroeopterin 3'-phosphate = (2R,3S)-3-(2-amino-4-oxo-1,4,7,8-tetrahydropteridin-6-yl)-2,3-dihydroxypropyl phosphate
7,8-dihydroneopterin 2'-phosphate = (1S,2R)-1-(2-amino-4-oxo-1,4,7,8-tetrahydropteridin-6-yl)-1,3-dihydroxypropan-2-yl phosphate
Other name(s): MptB
Systematic name: 7,8-dihydroneopterin 2',3'-cyclic phosphate 2'/3'-phosphodiesterase
Comments: Contains one zinc atom and one iron atom per subunit of the dodecameric enzyme. It hydrolyses 7,8-dihydroneopterin 2',3'-cyclic phosphate, a step in tetrahydromethanopterin biosynthesis. In vitro the enzyme forms 7,8-dihydroneopterin 2'-phosphate and 7,8-dihydroneopterin 3'-phosphate at a ratio of 4:1.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Mashhadi, Z., Xu, H. and White, R.H. An Fe2+-dependent cyclic phosphodiesterase catalyzes the hydrolysis of 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate in methanopterin biosynthesis. Biochemistry 48 (2009) 9384-9392. [PMID: 19746965]
Accepted name: phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase
Reaction: (1) 5-phospho-α-D-ribose 1,2-cyclic phosphate + H2O = D-ribofuranose 2,5-bisphosphate
(2) D-ribofuranose 2,5-bisphosphate + H2O = D-ribofuranose 5-phosphate + phosphate
Other name(s): cyclic phosphate dihydrolase; phnPP (gene name)
Systematic name: 5-phospho-α-D-ribose 1,2-cyclic phosphate 1,2-diphosphophosphohydrolase
Comments: The enzyme, characterized from the bacterium Eggerthella lenta, is involed in degradation of methylphosphonate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Ghodge, S.V., Cummings, J.A., Williams, H.J. and Raushel, F.M. Discovery of a cyclic phosphodiesterase that catalyzes the sequential hydrolysis of both ester bonds to phosphorus. J. Am. Chem. Soc. 135 (2013) 16360-16363. [PMID: 24147537]
Accepted name: RNA 2',3'-cyclic 3'-phosphodiesterase
Reaction: (ribonucleotide)n-2',3'-cyclic phosphate + H2O = (ribonucleotide)n-2'-phosphate
Other name(s): thpR (gene name); ligT (gene name)
Systematic name: (ribonucleotide)n-2',3'-cyclic phosphate 3'-nucleotidohydrolase
Comments: The enzyme hydrolyses RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester. In vitro the enzyme can also ligate tRNA molecules with 2',3'-cyclic phosphate to tRNA with 5'-hydroxyl termini, forming a 2'-5' phosphodiester linkage. However, the ligase activity is unlikely to be relevant in vivo.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Kanai, A., Sato, A., Fukuda, Y., Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kawai, G. and Tomita, M. Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus. RNA 15 (2009) 420-431. [PMID: 19155324]
2. Remus, B.S., Jacewicz, A. and Shuman, S. Structure and mechanism of E. coli RNA 2',3'-cyclic phosphodiesterase. RNA 20 (2014) 1697-1705. [PMID: 25239919]
Accepted name: cyclic-di-AMP phosphodiesterase
Reaction: cyclic di-3',5'-adenylate + H2O = 5'-O-phosphonoadenylyl-(3'→5')-adenosine
For diagram of reaction click here.
Glossary: cyclic di-3',5'-adenylate = cyclic bis(3'→5')diadenylate
5'-O-phosphonoadenylyl-(3'→5')-adenosine = pApA
Other name(s): gdpP (gene name)
Systematic name: cyclic bis(3'→5')diadenylate 3'-adenylylhydrolase
Comments: The enzyme, described from Gram-positive bacteria, degrades the second messenger cyclic di-3',5'-adenylate. It is a membrane-bound protein that contains a cytoplasmic facing Per-Arnt-Sim (PAS) domain, a modified GGDEF domain, and a DHH/DHHA1 domain, which confers the phosphodiesterase activity. Activity requires Mn2+ and is inhibited by pApA.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Rao, F., See, R.Y., Zhang, D., Toh, D.C., Ji, Q. and Liang, Z.X. YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity. J. Biol. Chem 285 (2010) 473-482. [PMID: 19901023]
2. Corrigan, R.M., Abbott, J.C., Burhenne, H., Kaever, V. and Grundling, A. c-di-AMP is a new second messenger in Staphylococcus aureus with a role in controlling cell size and envelope stress. PLoS Pathog. 7 (2011) e1002217. [PMID: 21909268]
3. Griffiths, J.M. and O'Neill, A.J. Loss of function of the gdpP protein leads to joint β-lactam/glycopeptide tolerance in Staphylococcus aureus. Antimicrob. Agents Chemother. 56 (2012) 579-581. [PMID: 21986827]
4. Bowman, L., Zeden, M.S., Schuster, C.F., Kaever, V. and Grundling, A. New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus. J. Biol. Chem 291 (2016) 26970-26986. [PMID: 27834680]
Accepted name: pApA phosphodiesterase
Reaction: 5'-O-phosphonoadenylyl-(3'→5')-adenosine + H2O = 2 AMP
For diagram of reaction click here.
Other name(s): pde2 (gene name); pApA hydrolase
Systematic name: 5'-O-phosphonoadenylyl-(3'→5')-adenosine phosphohydrolase
Comments: The enzyme, characterized from the Gram-positive bacterium Staphylococcus aureus, is a cytoplasmic protein that contains a DHH/DHHA1 domain. It can act on cyclic di-3',5'-adenylate with a much lower activity (cf. EC 3.1.4.59, cyclic-di-AMP phosphodiesterase). Activity requires Mn2+ and is inhibited by ppGpp.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:
References:
1. Bai, Y., Yang, J., Eisele, L.E., Underwood, A.J., Koestler, B.J., Waters, C.M., Metzger, D.W. and Bai, G. Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial growth and virulence. J. Bacteriol. 195 (2013) 5123-5132. [PMID: 24013631]
2. Ye, M., Zhang, J.J., Fang, X., Lawlis, G.B., Troxell, B., Zhou, Y., Gomelsky, M., Lou, Y. and Yang, X.F. DhhP, a cyclic di-AMP phosphodiesterase of Borrelia burgdorferi, is essential for cell growth and virulence. Infect. Immun. 82 (2014) 1840-1849. [PMID: 24566626]
3. Tang, Q., Luo, Y., Zheng, C., Yin, K., Ali, M.K., Li, X. and He, J. Functional analysis of a c-di-AMP-specific phosphodiesterase MsPDE from Mycobacterium smegmatis. Int J Biol Sci 11 (2015) 813-824. [PMID: 26078723]
4. Kuipers, K., Gallay, C., Martinek, V., Rohde, M., Martinkova, M., van der Beek, S.L., Jong, W.S., Venselaar, H., Zomer, A., Bootsma, H., Veening, J.W. and de Jonge, M.I. Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae. Mol. Microbiol. 101 (2016) 12-26. [PMID: 26691161]
5. Bowman, L., Zeden, M.S., Schuster, C.F., Kaever, V. and Grundling, A. New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus. J. Biol. Chem 291 (2016) 26970-26986. [PMID: 27834680]
Accepted name: cyclic 2,3-diphosphoglycerate hydrolase
Reaction: cyclic 2,3-bisphosphoglycerate + H2O = 2,3-diphosphoglycerate
Systematic name: cyclic 2,3-diphosphoglycerate phosphohydrolyase
Comments: The enzyme degrades cyclic 2,3-bisphosphoglycerate, a thermoprotectant that is produced by certain archaeal genera. Two different enzymes that catalyse this activity, one soluble and one membrane-bound, have been characterized from the archaeon Methanothermobacter thermautotrophicus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Sastry, M.V., Robertson, D.E., Moynihan, J.A. and Roberts, M.F. Enzymatic degradation of cyclic 2,3-diphosphoglycerate to 2,3-diphosphoglycerate in Methanobacterium thermoautotrophicum. Biochemistry 31 (1992) 2926-2935. [PMID: 1550819]
2. Alebeek G, J.WM., Kreuwels, M.JJ., Keltjens, J.T. and Vogels, G.D. Methanobacterium thermoautotrophicum (strain ΔH) contains a membrane-bound cyclic 2,3-diphosphoglycerate hydrolase. Arch. Microbiol. 161 (1994) 514-520.
Accepted name: phosphatidylethanolamine phospholipase C
Reaction: a phosphatidylethanolamine + H2O = a 1,2-diacyl-sn-glycerol + O-phosphoethanolamine
Other name(s): phosphatidylethanolamine-specific phospholipase C; PE-PLC; SMSr; SAMD8 (gene name); SMS1 (gene name)
Systematic name: phosphatidylethanolamine ethanolaminephosphohydrolase
Comments: This activity, which is similar to that of EC 3.1.4.3, phospholipase C, has been characterized from mammalian cells [1-4]. Multiple enzymes have been shown to catalyse this activity, including human sphingomyelin synthase-related protein (SMSr, gene name; SAMD8) [6-8] and sphingomyelin synthase 1 (SMS1, gene name; SGMS1) [9] (cf. EC 2.7.8.27, sphingomyelin synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Hafez, M.M. and Costlow, M.E. Phosphatidylethanolamine turnover is an early event in the response of NB2 lymphoma cells to prolactin. Exp. Cell Res. 184 (1989) 37-43. [PMID: 2507337]
2. Kiss, Z. and Anderson, W.B. ATP stimulates the hydrolysis of phosphatidylethanolamine in NIH 3T3 cells. Potentiating effects of guanosine triphosphates and sphingosine. J. Biol. Chem. 265 (1990) 7345-7350. [PMID: 2185245]
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