The Enzyme Database

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EC 3.1.4.51     
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]
[EC 3.1.4.51 created 1992]
 
 
EC 3.1.4.52     
Accepted name: cyclic-guanylate-specific phosphodiesterase
Reaction: cyclic di-3′,5′-guanylate + H2O = 5′-phosphoguanylyl(3′→5′)guanosine
For diagram of cyclic di-3′,5′-guanylate biosynthesis and breakdown, 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 (misleading); 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: 338732-46-0
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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 16081414]
[EC 3.1.4.52 created 2008]
 
 
EC 3.1.4.53     
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 (cf. EC 3.1.4.17, 3,5-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
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. [DOI] [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. [DOI] [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. [DOI] [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). [DOI] [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. [DOI] [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. [DOI] [PMID: 8810311]
[EC 3.1.4.53 created 2008, modified 2011]
 
 
EC 3.1.4.54     
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
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. [DOI] [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. [DOI] [PMID: 16527816]
[EC 3.1.4.54 created 2011]
 
 
EC 3.1.4.55     
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 phosphonate metabolism, 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
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. [DOI] [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. [DOI] [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. [DOI] [PMID: 21830807]
[EC 3.1.4.55 created 2013]
 
 
EC 3.1.4.56     
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 methanopterin biosynthesis (part 1), 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
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. [DOI] [PMID: 19746965]
[EC 3.1.4.56 created 2013]
 
 
EC 3.1.4.57     
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
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. [DOI] [PMID: 24147537]
[EC 3.1.4.57 created 2014]
 
 
EC 3.1.4.58     
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
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. [DOI] [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. [DOI] [PMID: 25239919]
[EC 3.1.4.58 created 2017]
 
 
EC 3.1.4.59     
Accepted name: cyclic-di-AMP phosphodiesterase
Reaction: cyclic di-3′,5′-adenylate + H2O = 5′-O-phosphonoadenylyl-(3′→5′)-adenosine
For diagram of cyclic di-3′,5′-adenylate biosynthesis and breakdown, 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, KEGG, MetaCyc, PDB
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:e1002217 (2011). [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]
[EC 3.1.4.59 created 2019]
 
 
EC 3.1.4.60     
Accepted name: pApA phosphodiesterase
Reaction: 5′-O-phosphonoadenylyl-(3′→5′)-adenosine + H2O = 2 AMP
For diagram of cyclic di-3′,5′-adenylate biosynthesis and breakdown, 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, KEGG, MetaCyc
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]
[EC 3.1.4.60 created 2019]
 
 
EC 3.1.4.61     
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
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. [DOI] [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. [DOI]
[EC 3.1.4.61 created 2021]
 
 


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