The Enzyme Database

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EC 2.4.2.30     
Accepted name: NAD+ ADP-ribosyltransferase
Reaction: NAD+ + (ADP-D-ribosyl)n-acceptor = nicotinamide + (ADP-D-ribosyl)n+1-acceptor + H+
For diagram of reaction, click here
Other name(s): poly(ADP-ribose) synthase; ADP-ribosyltransferase (polymerizing); NAD ADP-ribosyltransferase; PARP; PARP-1; NAD+:poly(adenine-diphosphate-D-ribosyl)-acceptor ADP-D-ribosyl-transferase (incorrect); NAD+:poly(adenosine-diphosphate-D-ribosyl)-acceptor ADP-D-ribosyl-transferase
Systematic name: NAD+:poly(ADP-D-ribosyl)-acceptor ADP-D-ribosyl-transferase
Comments: The ADP-D-ribosyl group of NAD+ is transferred to an acceptor carboxy group on a histone or the enzyme itself, and further ADP-ribosyl groups are transferred to the 2′-position of the terminal adenosine moiety, building up a polymer with an average chain length of 20–30 units.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 58319-92-9
References:
1.  Ueda, K. and Hayaishi, O. ADP-ribosylation. Annu. Rev. Biochem. 54 (1985) 73–100. [DOI] [PMID: 3927821]
2.  Ueda, K., Kawaichi, M. and Hayaishi, O. Poly(ADP-ribose) synthetase. In: Hayaishi, O. and Ueda, K. (Ed.), ADP-Ribosylation Reactions: Biology and Medicine, Academic Press, London, 1982, pp. 117–155.
3.  Ushiro, H., Yokoyama, Y. and Shizuta, Y. Purification and characterization of poly (ADP-ribose) synthetase from human placenta. J. Biol. Chem. 262 (1987) 2352–2357. [PMID: 2434482]
[EC 2.4.2.30 created 1984, modified 1990]
 
 
EC 2.4.2.37     
Accepted name: NAD+—dinitrogen-reductase ADP-D-ribosyltransferase
Reaction: NAD+ + [dinitrogen reductase]-L-arginine = nicotinamide + [dinitrogen reductase]-Nω-α-(ADP-D-ribosyl)-L-arginine
Other name(s): NAD-azoferredoxin (ADPribose)transferase; NAD-dinitrogen-reductase ADP-D-ribosyltransferase; draT (gene name)
Systematic name: NAD+:[dinitrogen reductase] (ADP-D-ribosyl)transferase
Comments: The combined action of this enzyme and EC 3.2.2.24, ADP-ribosyl-[dinitrogen reductase] hydrolase, controls the activity level of nitrogenase (EC 1.18.6.1). In the presence of ammonium, the product of nitrogenase, this enzyme covalently links an ADP-ribose moiety to a specific arginine residue of the dinitrogenase reductase component of nitrogenase, blocking its activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 117590-45-1
References:
1.  Lowery, R.G. and Ludden, P.W. Purification and properties of dinitrogenase reductase ADP-ribosyltransferase from the photosynthetic bacterium Rhodospirillum rubrum. J. Biol. Chem. 263 (1988) 16714–16719. [PMID: 3141411]
2.  Fitzmaurice, W.P., Saari, L.L., Lowery, R.G., Ludden, P.W. and Roberts, G.P. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Mol. Gen. Genet. 218 (1989) 340–347. [PMID: 2506427]
3.  Moure, V.R., Costa, F.F., Cruz, L.M., Pedrosa, F.O., Souza, E.M., Li, X.D., Winkler, F. and Huergo, L.F. Regulation of nitrogenase by reversible mono-ADP-ribosylation. Curr. Top. Microbiol. Immunol. 384 (2015) 89–106. [DOI] [PMID: 24934999]
[EC 2.4.2.37 created 1992, modified 2015]
 
 
EC 2.4.99.20     
Accepted name: 2′-phospho-ADP-ribosyl cyclase/2′-phospho-cyclic-ADP-ribose transferase
Reaction: NADP+ + nicotinate = nicotinate-adenine dinucleotide phosphate + nicotinamide (overall reaction)
(1a) NADP+ = 2′-phospho-cyclic ADP-ribose + nicotinamide
(1b) 2′-phospho-cyclic ADP-ribose + nicotinate = nicotinate-adenine dinucleotide phosphate
For diagram of cyclic ADP-ribose biosynthesis, click here
Glossary: 2′-phospho-cyclic ADP-ribose = cADPRP
nicotinic acid-adenine dinucleotide phosphate = NAADP+
Other name(s): diphosphopyridine nucleosidase (ambiguous); CD38 (gene name); BST1 (gene name)
Systematic name: NADP+:nicotinate ADP-ribosyltransferase
Comments: This multiunctional enzyme catalyses both the removal of nicotinamide from NADP+, forming 2′-phospho-cyclic ADP-ribose, and the addition of nicotinate to the cyclic product, forming NAADP+, a calcium messenger that can mobilize intracellular Ca2+ stores and activate Ca2+ influx to regulate a wide range of physiological processes. In addition, the enzyme also catalyses EC 3.2.2.6, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Chini, E.N., Chini, C.C., Kato, I., Takasawa, S. and Okamoto, H. CD38 is the major enzyme responsible for synthesis of nicotinic acid-adenine dinucleotide phosphate in mammalian tissues. Biochem. J. 362 (2002) 125–130. [PMID: 11829748]
2.  Moreschi, I., Bruzzone, S., Melone, L., De Flora, A. and Zocchi, E. NAADP+ synthesis from cADPRP and nicotinic acid by ADP-ribosyl cyclases. Biochem. Biophys. Res. Commun. 345 (2006) 573–580. [DOI] [PMID: 16690024]
[EC 2.4.99.20 created 2014]
 
 
EC 2.7.1.160     
Accepted name: 2′-phosphotransferase
Reaction: 2′-phospho-[ligated tRNA] + NAD+ = mature tRNA + ADP-ribose 1′′,2′′-phosphate + nicotinamide
For diagram of tRNA splicing, click here
Glossary: ADP-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
Other name(s): yeast 2′-phosphotransferase; Tpt1; Tpt1p; 2′-phospho-tRNA:NAD+ phosphotransferase
Systematic name: 2′-phospho-[ligated tRNA]:NAD+ phosphotransferase
Comments: Catalyses the final step of tRNA splicing in the yeast Saccharomyces cerevisiae [2]. The reaction takes place in two steps: in the first step, the 2′-phosphate on the RNA substrate is ADP-ribosylated, causing the relase of nicotinamide and the formation of the reaction intermediate, ADP-ribosylated tRNA [6]. In the second step, dephosphorylated (mature) tRNA is formed along with ADP ribose 1′′-2′′-cyclic phosphate. Highly specific for oligonucleotide substrates bearing an internal 2′-phosphate. Oligonucleotides with only a terminal 5′- or 3′-phosphate are not substrates [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 126905-00-8
References:
1.  Steiger, M.A., Kierzek, R., Turner, D.H. and Phizicky, E.M. Substrate recognition by a yeast 2′-phosphotransferase involved in tRNA splicing and by its Escherichia coli homolog. Biochemistry 40 (2001) 14098–14105. [DOI] [PMID: 11705403]
2.  Spinelli, S.L., Kierzek, R., Turner, D.H. and Phizicky, E.M. Transient ADP-ribosylation of a 2′-phosphate implicated in its removal from ligated tRNA during splicing in yeast. J. Biol. Chem. 274 (1999) 2637–2644. [DOI] [PMID: 9915792]
3.  Culver, G.M., McCraith, S.M., Consaul, S.A., Stanford, D.R. and Phizicky, E.M. A 2′-phosphotransferase implicated in tRNA splicing is essential in Saccharomyces cerevisiae. J. Biol. Chem. 272 (1997) 13203–13210. [DOI] [PMID: 9148937]
4.  McCraith, S.M. and Phizicky, E.M. An enzyme from Saccharomyces cerevisiae uses NAD+ to transfer the splice junction 2′-phosphate from ligated tRNA to an acceptor molecule. J. Biol. Chem. 266 (1991) 11986–11992. [PMID: 2050693]
5.  Hu, Q.D., Lu, H., Huo, K., Ying, K., Li, J., Xie, Y., Mao, Y. and Li, Y.Y. A human homolog of the yeast gene encoding tRNA 2′-phosphotransferase: cloning, characterization and complementation analysis. Cell. Mol. Life Sci. 60 (2003) 1725–1732. [DOI] [PMID: 14504659]
6.  Steiger, M.A., Jackman, J.E. and Phizicky, E.M. Analysis of 2′-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: evidence for a conserved two-step reaction mechanism. RNA 11 (2005) 99–106. [DOI] [PMID: 15611300]
7.  Sawaya, R., Schwer, B. and Shuman, S. Structure-function analysis of the yeast NAD+-dependent tRNA 2′-phosphotransferase Tpt1. RNA 11 (2005) 107–113. [DOI] [PMID: 15611301]
8.  Kato-Murayama, M., Bessho, Y., Shirouzu, M. and Yokoyama, S. Crystal structure of the RNA 2′-phosphotransferase from Aeropyrum pernix K1. J. Mol. Biol. 348 (2005) 295–305. [DOI] [PMID: 15811369]
[EC 2.7.1.160 created 2006]
 
 
EC 2.7.7.96     
Accepted name: ADP-D-ribose pyrophosphorylase
Reaction: ATP + D-ribose 5-phosphate = diphosphate + ADP-D-ribose
Other name(s): NUDIX5; NUDT5 (gene name); diphosphate—ADP-D-ribose adenylyltransferase; diphosphate adenylyltransferase (ambiguous)
Systematic name: ATP:D-ribose 5-phosphate adenylyltransferase
Comments: The human enzyme produces ATP in nuclei in situations of high energy demand, such as chromatin remodeling. The reaction is dependent on the presence of diphosphate. In its absence the enzyme catalyses the reaction of EC 3.6.1.13, ADP-ribose diphosphatase. cf. EC 2.7.7.35, ADP ribose phosphorylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wright, R.H., Lioutas, A., Le Dily, F., Soronellas, D., Pohl, A., Bonet, J., Nacht, A.S., Samino, S., Font-Mateu, J., Vicent, G.P., Wierer, M., Trabado, M.A., Schelhorn, C., Carolis, C., Macias, M.J., Yanes, O., Oliva, B. and Beato, M. ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling. Science 352 (2016) 1221–1225. [DOI] [PMID: 27257257]
[EC 2.7.7.96 created 2016]
 
 
EC 3.1.1.106     
Accepted name: O-acetyl-ADP-ribose deacetylase
Reaction: (1) 3′′-O-acetyl-ADP-D-ribose + H2O = ADP-D-ribose + acetate
(2) 2′′-O-acetyl-ADP-D-ribose + H2O = ADP-D-ribose + acetate
Other name(s): ymdB (gene name); MACROD1 (gene name)
Systematic name: O-acetyl-ADP-D-ribose carboxylesterase
Comments: The enzyme, characterized from the bacterium Escherichia coli and from human cells, removes the acetyl group from either the 2′′ or 3′′ position of O-acetyl-ADP-ribose, which are formed by the action of EC 2.3.1.286, protein acetyllysine N-acetyltransferase. The human enzyme can also remove ADP-D-ribose from phosphorylated double stranded DNA adducts.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Chen, D., Vollmar, M., Rossi, M.N., Phillips, C., Kraehenbuehl, R., Slade, D., Mehrotra, P.V., von Delft, F., Crosthwaite, S.K., Gileadi, O., Denu, J.M. and Ahel, I. Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J. Biol. Chem. 286 (2011) 13261–13271. [PMID: 21257746]
2.  Zhang, W., Wang, C., Song, Y., Shao, C., Zhang, X. and Zang, J. Structural insights into the mechanism of Escherichia coli YmdB: A 2′-O-acetyl-ADP-ribose deacetylase. J. Struct. Biol. 192 (2015) 478–486. [PMID: 26481419]
3.  Agnew, T., Munnur, D., Crawford, K., Palazzo, L., Mikoc, A. and Ahel, I. MacroD1 is a promiscuous ADP-ribosyl hydrolase localized to mitochondria. Front. Microbiol. 9:20 (2018). [PMID: 29410655]
[EC 3.1.1.106 created 2019]
 
 
EC 3.1.3.84     
Accepted name: ADP-ribose 1′′-phosphate phosphatase
Reaction: ADP-D-ribose 1′′-phosphate + H2O = ADP-D-ribose + phosphate
Other name(s): POA1; Appr1p phosphatase; Poa1p; ADP-ribose 1′′-phosphate phosphohydrolase
Systematic name: ADP-D-ribose 1′′-phosphate phosphohydrolase
Comments: The enzyme is highly specific for ADP-D-ribose 1′′-phosphate. Involved together with EC 3.1.4.37, 2′,3′-cyclic-nucleotide 3′-phosphodiesterase, in the breakdown of adenosine diphosphate ribose 1′′,2′′-cyclic phosphate (Appr>p), a by-product of tRNA splicing.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Shull, N.P., Spinelli, S.L. and Phizicky, E.M. A highly specific phosphatase that acts on ADP-ribose 1′′-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res. 33 (2005) 650–660. [DOI] [PMID: 15684411]
[EC 3.1.3.84 created 2011]
 
 
EC 3.2.1.143     
Accepted name: poly(ADP-ribose) glycohydrolase
Reaction: hydrolyses poly(ADP-D-ribose) at glycosidic (1′′-2′) linkage of ribose-ribose bond to produce free ADP-D-ribose
For diagram of reaction, click here
Glossary: ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
Comments: Specific to (1′′-2′) linkage of ribose-ribose bond of poly(ADP-D-ribose).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9068-16-0
References:
1.  Miwa, M. and Sugimura, T. Splitting of the ribose-ribose linkage of poly(adenosine diphosphate-ribose) by a calf thymus extract. J. Biol. Chem. 246 (1971) 6362–6364. [PMID: 4331388]
2.  Lin, W., Ame, J.C., Aboul-Ela, N., Jacobson, E.L. and Jacobson, M.K. Isolation and characterization of the cDNA encoding bovine poly(ADP-ribose) glycohydrolase. J. Biol. Chem. 272 (1997) 11895–11901. [DOI] [PMID: 9115250]
[EC 3.2.1.143 created 2000]
 
 
EC 3.2.2.5     
Accepted name: NAD+ glycohydrolase
Reaction: NAD+ + H2O = ADP-D-ribose + nicotinamide
Glossary: ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
Other name(s): NAD glycohydrolase; nicotinamide adenine dinucleotide glycohydrolase; β-NAD+ glycohydrolase; DPNase (ambiguous); NAD hydrolase (ambiguous); diphosphopyridine nucleosidase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD nucleosidase (ambiguous); DPN hydrolase (ambiguous); NADase (ambiguous); nga (gene name); NAD+ nucleosidase
Systematic name: NAD+ glycohydrolase
Comments: This enzyme catalyses the hydrolysis of NAD+, without associated ADP-ribosyl cyclase activity (unlike the metazoan enzyme EC 3.2.2.6, bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase). The enzyme from Group A streptococci has been implicated in the pathogenesis of diseases such as streptococcal toxic shock-like syndrome (STSS) and necrotizing fasciitis. The enzyme from the venom of the snake Agkistrodon acutus also catalyses EC 3.6.1.5, apyrase [3].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9025-46-1
References:
1.  Fehrenbach, F.J. Reinigung und Kristallisation der NAD-Glykohydrolase aus C-Streptokokken. Eur. J. Biochem. 18 (1971) 94–102. [DOI] [PMID: 4322210]
2.  Grushoff, P.S., Shany, S. and Bernheimer, A.W. Purification and properties of streptococcal nicotinamide adenine dinucleotide glycohydrolase. J. Bacteriol. 122 (1975) 599–605. [PMID: 236282]
3.  Zhang, L., Xu, X., Luo, Z., Shen, D. and Wu, H. Identification of an unusual AT(D)Pase-like activity in multifunctional NAD glycohydrolase from the venom of Agkistrodon acutus. Biochimie 91 (2009) 240–251. [DOI] [PMID: 18952139]
4.  Ghosh, J., Anderson, P.J., Chandrasekaran, S. and Caparon, M.G. Characterization of Streptococcus pyogenes β-NAD+ glycohydrolase: re-evaluation of enzymatic properties associated with pathogenesis. J. Biol. Chem. 285 (2010) 5683–5694. [DOI] [PMID: 20018886]
5.  Smith, C.L., Ghosh, J., Elam, J.S., Pinkner, J.S., Hultgren, S.J., Caparon, M.G. and Ellenberger, T. Structural basis of Streptococcus pyogenes immunity to its NAD+ glycohydrolase toxin. Structure 19 (2011) 192–202. [DOI] [PMID: 21300288]
[EC 3.2.2.5 created 1961, modified 2013]
 
 
EC 3.2.2.6     
Accepted name: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Reaction: NAD+ + H2O = ADP-D-ribose + nicotinamide (overall reaction)
(1a) NAD+ = cyclic ADP-ribose + nicotinamide
(1b) cyclic ADP-ribose + H2O = ADP-D-ribose
For diagram of cyclic ADP-ribose biosynthesis, click here
Glossary: ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
cyclic ADP-ribose = N1-(β-D-ribosyl)adenosine 5′(P1),5′′(P2)-cyclic diphosphate
Other name(s): NAD+ nucleosidase; NADase (ambiguous); DPNase (ambiguous); DPN hydrolase (ambiguous); NAD hydrolase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD glycohydrolase (misleading); NAD nucleosidase (ambiguous); nicotinamide adenine dinucleotide glycohydrolase (misleading); CD38 (gene name); BST1 (gene name)
Systematic name: NAD+ glycohydrolase (cyclic ADP-ribose-forming)
Comments: This multiunctional enzyme acts on NAD+, catalysing both the synthesis and hydrolysis of cyclic ADP-ribose, a calcium messenger that can mobilize intracellular Ca2+ stores and activate Ca2+ influx to regulate a wide range of physiological processes. In addition, the enzyme also catalyses EC 2.4.99.20, 2′-phospho-ADP-ribosyl cyclase/2′-phospho-cyclic-ADP-ribose transferase. It is also able to act on β-nicotinamide D-ribonucleotide. cf. EC 3.2.2.5, NAD+ glycohydrolase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9032-65-9
References:
1.  Imai, T. Purification and characterization of a pyridine nucleotide glycohydrolase from rabbit spleen. J. Biochem. 106 (1989) 928–937. [PMID: 2613697]
2.  Howard, M., Grimaldi, J.C., Bazan, J.F., Lund, F.E., Santos-Argumedo, L., Parkhouse, R.M., Walseth, T.F. and Lee, H.C. Formation and hydrolysis of cyclic ADP-ribose catalyzed by lymphocyte antigen CD38. Science 262 (1993) 1056–1059. [DOI] [PMID: 8235624]
3.  Takasawa, S., Tohgo, A., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Yonekura, H. and Okamoto, H. Synthesis and hydrolysis of cyclic ADP-ribose by human leukocyte antigen CD38 and inhibition of the hydrolysis by ATP. J. Biol. Chem. 268 (1993) 26052–26054. [PMID: 8253715]
4.  Tohgo, A., Takasawa, S., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Furuya, Y., Yonekura, H. and Okamoto, H. Essential cysteine residues for cyclic ADP-ribose synthesis and hydrolysis by CD38. J. Biol. Chem. 269 (1994) 28555–28557. [PMID: 7961800]
5.  Fryxell, K.B., O'Donoghue, K., Graeff, R.M., Lee, H.C. and Branton, W.D. Functional expression of soluble forms of human CD38 in Escherichia coli and Pichia pastoris. Protein Expr. Purif. 6 (1995) 329–336. [DOI] [PMID: 7663169]
6.  Yamamoto-Katayama, S., Ariyoshi, M., Ishihara, K., Hirano, T., Jingami, H. and Morikawa, K. Crystallographic studies on human BST-1/CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities. J. Mol. Biol. 316 (2002) 711–723. [DOI] [PMID: 11866528]
7.  Liu, Q., Kriksunov, I.A., Graeff, R., Munshi, C., Lee, H.C. and Hao, Q. Crystal structure of human CD38 extracellular domain. Structure 13 (2005) 1331–1339. [DOI] [PMID: 16154090]
[EC 3.2.2.6 created 1961, modified 2004, modified 2014, modified 2018]
 
 
EC 3.2.2.14     
Accepted name: NMN nucleosidase
Reaction: β-nicotinamide D-ribonucleotide + H2O = D-ribose 5-phosphate + nicotinamide
Other name(s): NMNase; nicotinamide mononucleotide nucleosidase; nicotinamide mononucleotidase; NMN glycohydrolase; NMNGhase
Systematic name: nicotinamide-nucleotide phosphoribohydrolase
Comments: The enzyme is thought to participate in an NAD+-salvage pathway. In eukaryotic organisms this activity has been attributed to EC 3.2.2.6, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37237-49-3
References:
1.  Andreoli, A.J., Okita, T.W., Bloom, R. and Grover, T.A. The pyridine nucleotide cycle: presence of a nicotinamide mononucleotide-specific glycohydrolase in Escherichia coli. Biochem. Biophys. Res. Commun. 49 (1972) 264–269. [DOI] [PMID: 4342726]
2.  Imai, T. Isolation and properties of a glycohydrolase specific for nicotinamide mononucleotide from Azotobacter vinelandii. J. Biochem. 85 (1979) 887–899. [PMID: 457634]
3.  Imai, T. Properties of allosteric nicotinamide mononucleotide glycohydrolase from Azotobacter vinelandii: activation and inhibition. J. Biochem. 101 (1987) 163–173. [PMID: 3571198]
[EC 3.2.2.14 created 1976, modified 2018]
 
 
EC 3.2.2.19     
Accepted name: [protein ADP-ribosylarginine] hydrolase
Reaction: (1) protein-Nω-(ADP-D-ribosyl)-L-arginine + H2O = ADP-D-ribose + protein-L-arginine
(2) Nω-(ADP-D-ribosyl)-L-arginine + H2O = ADP-D-ribose + L-arginine
Glossary: ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
Other name(s): ADP-ribose-L-arginine cleavage enzyme; ADP-ribosylarginine hydrolase; Nω-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase; protein-ω-N-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase
Systematic name: protein-Nω-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase
Comments: The enzyme will remove ADP-D-ribose from arginine residues in ADP-ribosylated proteins.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 98668-52-1
References:
1.  Moss, J., Jacobson, M.K. and Stanley, S.J. Reversibility of arginine-specific mono(ADP-ribosyl)ation: identification in erythrocytes of an ADP-ribose-L-arginine cleavage enzyme. Proc. Natl. Acad. Sci. USA 82 (1985) 5603–5607. [DOI] [PMID: 2994036]
2.  Moss, J., Stanley, S.J., Nightingale, M.S., Murtagh, J.J., Jr., Monaco, L., Mishima, K., Chen, H.C., Williamson, K.C. and Tsai, S.C. Molecular and immunological characterization of ADP-ribosylarginine hydrolases. J. Biol. Chem. 267 (1992) 10481–10488. [PMID: 1375222]
3.  Konczalik, P. and Moss, J. Identification of critical, conserved vicinal aspartate residues in mammalian and bacterial ADP-ribosylarginine hydrolases. J. Biol. Chem. 274 (1999) 16736–16740. [DOI] [PMID: 10358013]
4.  Takada, T., Iida, K. and Moss, J. Cloning and site-directed mutagenesis of human ADP-ribosylarginine hydrolase. J. Biol. Chem. 268 (1993) 17837–17843. [PMID: 8349667]
5.  Ohno, T., Tsuchiya, M., Osago, H., Hara, N., Jidoi, J. and Shimoyama, M. Detection of arginine-ADP-ribosylated protein using recombinant ADP-ribosylarginine hydrolase. Anal. Biochem. 10 (1995) 115–122. [DOI] [PMID: 8678289]
[EC 3.2.2.19 created 1989, modified 2004]
 
 
EC 3.2.2.24     
Accepted name: ADP-ribosyl-[dinitrogen reductase] hydrolase
Reaction: [dinitrogen reductase]-Nω-α-(ADP-D-ribosyl)-L-arginine = ADP-D-ribose + [dinitrogen reductase]-L-arginine
Other name(s): azoferredoxin glycosidase; azoferredoxin-activating enzymes; dinitrogenase reductase-activating glycohydrolase; ADP-ribosyl glycohydrolase; draG (gene name)
Systematic name: ADP-D-ribosyl-[dinitrogen reductase] ADP-ribosylhydrolase
Comments: The enzyme restores the activity of EC 1.18.6.1, nitrogenase, by catalysing the removal of ADP-ribose from an arginine residue of the dinitrogenase reductase component of nitrogenase. This activity occurs only when the nitrogenase product, ammonium, is not available. The combined activity of this enzyme and EC 2.4.2.37, NAD+-dinitrogen-reductase ADP-D-ribosyltransferase, controls the level of activity of nitrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 125626-63-3
References:
1.  Fitzmaurice, W.P., Saari, L.L., Lowery, R.G., Ludden, P.W. and Roberts, G.P. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Mol. Gen. Genet. 218 (1989) 340–347. [PMID: 2506427]
2.  Li, X.D., Huergo, L.F., Gasperina, A., Pedrosa, F.O., Merrick, M. and Winkler, F.K. Crystal structure of dinitrogenase reductase-activating glycohydrolase (DraG) reveals conservation in the ADP-ribosylhydrolase fold and specific features in the ADP-ribose-binding pocket. J. Mol. Biol. 390 (2009) 737–746. [DOI] [PMID: 19477184]
3.  Berthold, C.L., Wang, H., Nordlund, S. and Hogbom, M. Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG. Proc. Natl. Acad. Sci. USA 106 (2009) 14247–14252. [DOI] [PMID: 19706507]
[EC 3.2.2.24 created 1992]
 
 
EC 3.4.22.56     
Accepted name: caspase-3
Reaction: Strict requirement for an Asp residue at positions P1 and P4. It has a preferred cleavage sequence of Asp-Xaa-Xaa-Asp┼ with a hydrophobic amino-acid residue at P2 and a hydrophilic amino-acid residue at P3, although Val or Ala are also accepted at this position
Other name(s): CPP32; apopain; yama protein
Comments: Caspase-3 is an effector/executioner caspase, as are caspase-6 (EC 3.4.22.59) and caspase-7 (EC 3.4.22.60) [5]. These caspases are responsible for the proteolysis of the majority of cellular polypeptides [e.g. poly(ADP-ribose) polymerase (PARP)], which leads to the apoptotic phenotype [3,5]. Procaspase-3 can be activated by caspase-1 (EC 3.4.22.36), caspase-8 (EC 3.4.22.61), caspase-9 (EC 3.4.22.62) and caspase-10 (EC 3.4.22.63) as well as by the serine protease granzyme B [1]. Caspase-3 can activate procaspase-2 (EC 3.4.22.55) [2]. Activation occurs by inter-domain cleavage followed by removal of the N-terminal prodomain [6]. Although Asp-Glu-(Val/Ile)-Asp is thought to be the preferred cleavage sequence, the enzyme can accommodate different residues at P2 and P3 of the substrate [4]. Like caspase-2, a hydrophobic residue at P5 of caspase-3 leads to more efficient hydrolysis, e.g. (Val/Leu)-Asp-Val-Ala-Asp┼ is a better substrate than Asp-Val-Ala-Asp┼ . This is not the case for caspase-7 [4]. Belongs in peptidase family C14.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 169592-56-7
References:
1.  Krebs, J.F., Srinivasan, A., Wong, A.M., Tomaselli, K.J., Fritz, L.C. and Wu, J.C. Heavy membrane-associated caspase 3: identification, isolation, and characterization. Biochemistry 39 (2000) 16056–16063. [DOI] [PMID: 11123933]
2.  Li, H., Bergeron, L., Cryns, V., Pasternack, M.S., Zhu, H., Shi, L., Greenberg, A. and Yuan, J. Activation of caspase-2 in apoptosis. J. Biol. Chem. 272 (1997) 21010–21017. [DOI] [PMID: 9261102]
3.  Nicholson, D. and Thornberry, N.A. Caspase-3 and caspase-7. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Ed.), Handbook of Proteolytic Enzymes, 2nd edn, Elsevier, London, 2004, pp. 1298–1302.
4.  Fang, B., Boross, P.I., Tozser, J. and Weber, I.T. Structural and kinetic analysis of caspase-3 reveals role for S5 binding site in substrate recognition. J. Mol. Biol. 360 (2006) 654–666. [DOI] [PMID: 16781734]
5.  Chang, H.Y. and Yang, X. Proteases for cell suicide: functions and regulation of caspases. Microbiol. Mol. Biol. Rev. 64 (2000) 821–846. [PMID: 11104820]
6.  Martin, S.J., Amarante-Mendes, G.P., Shi, L., Chuang, T.H., Casiano, C.A., O'Brien, G.A., Fitzgerald, P., Tan, E.M., Bokoch, G.M., Greenberg, A.H. and Green, D.R. The cytotoxic cell protease granzyme B initiates apoptosis in a cell-free system by proteolytic processing and activation of the ICE/CED-3 family protease, CPP32, via a novel two-step mechanism. EMBO J. 15 (1996) 2407–2416. [PMID: 8665848]
[EC 3.4.22.56 created 2007]
 
 
EC 3.4.22.59     
Accepted name: caspase-6
Reaction: Strict requirement for Asp at position P1 and has a preferred cleavage sequence of Val-Glu-His-Asp┼
Other name(s): CASP-6; apoptotic protease Mch-2; Mch2
Comments: Caspase-6 is an effector/executioner caspase, as are caspase-3 (EC 3.4.22.56) and caspase-7 (EC 3.4.22.60) [2]. These caspases are responsible for the proteolysis of the majority of cellular polypeptides [e.g. poly(ADP-ribose) polymerase (PARP)], which leads to the apoptotic phenotype [2]. Caspase-6 can cleave its prodomain to produce mature caspase-6, which directly activates caspase-8 (EC 3.4.22.61) and leads to the release of cytochrome c from the mitochondria. The release of cytochrome c is an essential component of the intrinsic apoptosis pathway [1]. The enzyme can also cleave and inactivate lamins, the intermediate filament scaffold proteins of the nuclear envelope, leading to nuclear fragmentation in the final phases of apoptosis [2,4,5,6]. Belongs in peptidase family C14.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 182372-15-2
References:
1.  Cowling, V. and Downward, J. Caspase-6 is the direct activator of caspase-8 in the cytochrome c-induced apoptosis pathway: absolute requirement for removal of caspase-6 prodomain. Cell Death Differ. 9 (2002) 1046–1056. [DOI] [PMID: 12232792]
2.  Chang, H.Y. and Yang, X. Proteases for cell suicide: functions and regulation of caspases. Microbiol. Mol. Biol. Rev. 64 (2000) 821–846. [PMID: 11104820]
3.  Kang, B.H., Ko, E., Kwon, O.K. and Choi, K.Y. The structure of procaspase 6 is similar to that of active mature caspase 6. Biochem. J. 364 (2002) 629–634. [DOI] [PMID: 12049625]
4.  Lee, S.C., Chan, J., Clement, M.V. and Pervaiz, S. Functional proteomics of resveratrol-induced colon cancer cell apoptosis: caspase-6-mediated cleavage of lamin A is a major signaling loop. Proteomics 6 (2006) 2386–2394. [DOI] [PMID: 16518869]
5.  MacLachlan, T.K. and El-Deiry, W.S. Apoptotic threshold is lowered by p53 transactivation of caspase-6. Proc. Natl. Acad. Sci. USA 99 (2002) 9492–9497. [DOI] [PMID: 12089322]
6.  Takahashi, A., Alnemri, E.S., Lazebnik, Y.A., Fernandes-Alnemri, T., Litwack, G., Moir, R.D., Goldman, R.D., Poirier, G.G., Kaufmann, S.H. and Earnshaw, W.C. Cleavage of lamin A by Mch2α but not CPP32: multiple interleukin 1β-converting enzyme-related proteases with distinct substrate recognition properties are active in apoptosis. Proc. Natl. Acad. Sci. USA 93 (1996) 8395–8400. [DOI] [PMID: 8710882]
[EC 3.4.22.59 created 2007]
 
 
EC 3.4.22.60     
Accepted name: caspase-7
Reaction: Strict requirement for an Asp residue at position P1 and has a preferred cleavage sequence of Asp-Glu-Val-Asp┼
Other name(s): CASP-7; ICE-like apoptotic protease 3; ICE-LAP3; apoptotic protease Mch-3; Mch3; CMH-1
Comments: Caspase-7 is an effector/executioner caspase, as are caspase-3 (EC 3.4.22.56) and caspase-6 (EC 3.4.22.59) [1]. These caspases are responsible for the proteolysis of the majority of cellular polypeptides [e.g. poly(ADP-ribose) polymerase (PARP)], which leads to the apoptotic phenotype [2]. Although a hydrophobic residue at P5 of caspase-2 (EC 3.4.22.55) and caspase-3 leads to more efficient hydrolysis, the amino-acid residue at this location in caspase-7 has no effect [3]. Caspase-7 is activated by the initiator caspases [caspase-8 (EC 3.4.22.61), caspase-9 (EC 3.4.22.62) and caspase-10 (EC 3.4.22.63)]. Removal of the N-terminal prodomain occurs before cleavage in the linker region between the large and small subunits [4]. Belongs in peptidase family C14.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 189258-14-8
References:
1.  Chang, H.Y. and Yang, X. Proteases for cell suicide: functions and regulation of caspases. Microbiol. Mol. Biol. Rev. 64 (2000) 821–846. [PMID: 11104820]
2.  Nicholson, D. and Thornberry, N.A. Caspase-3 and caspase-7. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Ed.), Handbook of Proteolytic Enzymes, 2nd edn, Elsevier, London, 2004, pp. 1298–1302.
3.  Fang, B., Boross, P.I., Tozser, J. and Weber, I.T. Structural and kinetic analysis of caspase-3 reveals role for S5 binding site in substrate recognition. J. Mol. Biol. 360 (2006) 654–666. [DOI] [PMID: 16781734]
4.  Denault, J.B. and Salvesen, G.S. Human caspase-7 activity and regulation by its N-terminal peptide. J. Biol. Chem. 278 (2003) 34042–34050. [DOI] [PMID: 12824163]
[EC 3.4.22.60 created 2007]
 
 
EC 3.6.1.13     
Accepted name: ADP-ribose diphosphatase
Reaction: ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
Glossary: ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
Other name(s): ADPribose pyrophosphatase; adenosine diphosphoribose pyrophosphatase; ADPR-PPase; ADP-ribose ribophosphohydrolase
Systematic name: ADP-D-ribose ribophosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-83-3
References:
1.  Doherty, M.D. and Morrison, J.F. The hydrolysis of adenosine diphosphate ribose by a specific phosphohydrolase of rabbit-muscle extracts. Biochim. Biophys. Acta 65 (1962) 364–366. [DOI] [PMID: 14028386]
[EC 3.6.1.13 created 1965]
 
 
EC 3.6.1.53     
Accepted name: Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
Reaction: (1) CDP-choline + H2O = CMP + phosphocholine
(2) ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
Other name(s): Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase; ADPRibase-Mn
Systematic name: CDP-choline phosphohydrolase
Comments: Requires Mn2+. Unlike EC 3.6.1.13, ADP-ribose diphosphatase, it cannot utilize Mg2+. ADP-D-ribose, CDP-choline, CDP-ethanolamine and ADP are substrates for this enzyme but ADP-D-glucose, UDP-D-glucose, CDP-D-glucose, CDP, CMP and AMP are not hydrolysed [2]. The mammalian enzyme hydrolyses cyclic ADP-ribose to 1-(5-phospho-β-D-ribosyl)-AMP with ~100-fold lower efficiency than ADP-D-ribose [3]. In rat, the enzyme is found predominantly in thymus and spleen.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Canales, J., Pinto, R.M., Costas, M.J., Hernández, M.T., Miró, A., Bernet, D., Fernández, A. and Cameselle, J.C. Rat liver nucleoside diphosphosugar or diphosphoalcohol pyrophosphatases different from nucleotide pyrophosphatase or phosphodiesterase I: substrate specificities of Mg2+-and/or Mn2+-dependent hydrolases acting on ADP-ribose. Biochim. Biophys. Acta 1246 (1995) 167–177. [DOI] [PMID: 7819284]
2.  Canales, J., Fernández, A., Ribeiro, J.M., Cabezas, A., Rodrigues, J.R., Cameselle, J.C. and Costas, M.J. Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase: a novel metallophosphoesterase family preferentially expressed in rodent immune cells. Biochem. J. 413 (2008) 103–113. [DOI] [PMID: 18352857]
3.  Canales, J., Fernandez, A., Rodrigues, J.R., Ferreira, R., Ribeiro, J.M., Cabezas, A., Costas, M.J. and Cameselle, J.C. Hydrolysis of the phosphoanhydride linkage of cyclic ADP-ribose by the Mn(2+)-dependent ADP-ribose/CDP-alcohol pyrophosphatase. FEBS Lett. 583 (2009) 1593–1598. [DOI] [PMID: 19379742]
4.  Rodrigues, J.R., Fernandez, A., Canales, J., Cabezas, A., Ribeiro, J.M., Costas, M.J. and Cameselle, J.C. Characterization of Danio rerio Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase, the structural prototype of the ADPRibase-Mn-like protein family. PLoS One 7:e42249 (2012). [DOI] [PMID: 22848751]
[EC 3.6.1.53 created 2008]
 
 
EC 3.6.1.58     
Accepted name: 8-oxo-dGDP phosphatase
Reaction: (1) 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate
(2) 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate
Glossary: 8-oxo-dGDP = 8-oxo-7,8-dihydro-2′-deoxyguanosine 5′-diphosphate
Other name(s): NUDT5; MTH3 (gene name); NUDT18
Systematic name: 8-oxo-dGDP phosphohydrolase
Comments: The enzyme catalyses the hydrolysis of both 8-oxo-dGDP and 8-oxo-GDP thereby preventing translational errors caused by oxidative damage. The preferred in vivo substrate is not known. The enzyme does not degrade 8-oxo-dGTP and 8-oxo-GTP to the monophosphates (cf. EC 3.6.1.55, 8-oxo-dGTP diphosphatase) [1,2]. Ribonucleotide diphosphates and deoxyribonucleotide diphosphates are hydrolysed with broad specificity. The bifunctional enzyme NUDT5 also hydrolyses ADP-ribose to AMP and D-ribose 5-phosphate (cf. EC 3.6.1.13, ADP-ribose diphosphatase) [4]. The human enzyme NUDT18 also hydrolyses 8-oxo-dADP and 2-hydroxy-dADP, the latter at a slower rate [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ishibashi, T., Hayakawa, H., Ito, R., Miyazawa, M., Yamagata, Y. and Sekiguchi, M. Mammalian enzymes for preventing transcriptional errors caused by oxidative damage. Nucleic Acids Res. 33 (2005) 3779–3784. [DOI] [PMID: 16002790]
2.  Ishibashi, T., Hayakawa, H. and Sekiguchi, M. A novel mechanism for preventing mutations caused by oxidation of guanine nucleotides. EMBO Rep. 4 (2003) 479–483. [DOI] [PMID: 12717453]
3.  Kamiya, H., Hori, M., Arimori, T., Sekiguchi, M., Yamagata, Y. and Harashima, H. NUDT5 hydrolyzes oxidized deoxyribonucleoside diphosphates with broad substrate specificity. DNA Repair (Amst) 8 (2009) 1250–1254. [DOI] [PMID: 19699693]
4.  Ito, R., Sekiguchi, M., Setoyama, D., Nakatsu, Y., Yamagata, Y. and Hayakawa, H. Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein. J. Biochem. 149 (2011) 731–738. [DOI] [PMID: 21389046]
5.  Zha, M., Zhong, C., Peng, Y., Hu, H. and Ding, J. Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity. J. Mol. Biol. 364 (2006) 1021–1033. [DOI] [PMID: 17052728]
6.  Takagi, Y., Setoyama, D., Ito, R., Kamiya, H., Yamagata, Y. and Sekiguchi, M. Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2. J. Biol. Chem. 287 (2012) 21541–21549. [DOI] [PMID: 22556419]
[EC 3.6.1.58 created 2012]
 
 


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