The Enzyme Database

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EC 2.7.7.85     
Accepted name: diadenylate cyclase
Reaction: 2 ATP = 2 diphosphate + cyclic di-3′,5′-adenylate
Glossary: cyclic di-3′,5′-adenylate = c-di-AMP = c-di-adenylate = cyclic-bis(3′→5′) dimeric AMP
Other name(s): cyclic-di-AMP synthase; dacA (gene name); disA (gene name)
Systematic name: ATP:ATP adenylyltransferase (cyclizing)
Comments: Cyclic di-3′,5′-adenylate is a bioactive molecule produced by some bacteria and archaea, which may function as a secondary signalling molecule [1]. The intracellular bacterial pathogen Listeria monocytogenes secretes it into the host’s cytosol, where it triggers a cytosolic pathway of innate immunity [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Witte, G., Hartung, S., Buttner, K. and Hopfner, K.P. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol. Cell 30 (2008) 167–178. [DOI] [PMID: 18439896]
2.  Woodward, J.J., Iavarone, A.T. and Portnoy, D.A. c-di-AMP secreted by intracellular Listeria monocytogenes activates a host type I interferon response. Science 328 (2010) 1703–1705. [DOI] [PMID: 20508090]
[EC 2.7.7.85 created 2013]
 
 
EC 3.1.4.59     
Accepted name: cyclic-di-AMP phosphodiesterase
Reaction: cyclic di-3′,5′-adenylate + H2O = 5′-O-phosphonoadenylyl-(3′→5′)-adenosine
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
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
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]
 
 


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