The Enzyme Database

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EC 2.1.1.98     
Accepted name: diphthine synthase
Reaction: 3 S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = 3 S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2] (overall reaction)
(1a) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2]
(1b) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2]
(1c) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Glossary: diphthine = 2-[(3S)-3-carboxy-3-(trimethylamino)propyl]-L-histidine
Other name(s): S-adenosyl-L-methionine:elongation factor 2 methyltransferase (ambiguous); diphthine methyltransferase (ambiguous); S-adenosyl-L-methionine:2-(3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] methyltransferase; Dph5 (ambiguous)
Systematic name: S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine-[translation elongation factor 2]-forming)
Comments: This archaeal enzyme produces the trimethylated product diphthine, which is converted into diphthamide by EC 6.3.1.14, diphthine—ammonia ligase. Different from the eukaryotic enzyme, which produces diphthine methyl ester (cf. EC 2.1.1.314). In the archaeon Pyrococcus horikoshii the enzyme acts on His600 of elongation factor 2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 114514-25-9
References:
1.  Zhu, X., Kim, J., Su, X. and Lin, H. Reconstitution of diphthine synthase activity in vitro. Biochemistry 49 (2010) 9649–9657. [DOI] [PMID: 20873788]
[EC 2.1.1.98 created 1990, modified 2013, modified 2015]
 
 
EC 2.1.1.314     
Accepted name: diphthine methyl ester synthase
Reaction: 4 S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = 4 S-adenosyl-L-homocysteine + diphthine methyl ester-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Glossary: diphthine methyl ester = 2-[(3S)-4-methoxy-4-oxo-3-(trimethylammonio)butyl]-L-histidine
Other name(s): S-adenosyl-L-methionine:elongation factor 2 methyltransferase (ambiguous); diphthine methyltransferase (ambiguous); Dph5 (ambiguous)
Systematic name: S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine methyl ester-[translation elongation factor 2]-forming)
Comments: This eukaryotic enzyme is part of the biosynthetic pathway of diphthamide. Different from the archaeal enzyme, which performs only 3 methylations, producing diphthine (cf. EC 2.1.1.98). The relevant histidine of elongation factor 2 is His715 in mammals and His699 in yeast. The order of the 4 methylations is not known.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Chen, J.-Y.C. and Bodley, J.W. Biosynthesis of diphthamide in Saccharomyces cerevisiae. Partial purification and characterization of a specific S-adenosylmethionine:elongation factor 2 methyltransferase. J. Biol. Chem. 263 (1988) 11692–11696. [PMID: 3042777]
2.  Moehring, J.M. and Moehring, T.J. The post-translational trimethylation of diphthamide studied in vitro. J. Biol. Chem. 263 (1988) 3840–3844. [PMID: 3346227]
3.  Lin, Z., Su, X., Chen, W., Ci, B., Zhang, S. and Lin, H. Dph7 catalyzes a previously unknown demethylation step in diphthamide biosynthesis. J. Am. Chem. Soc. 136 (2014) 6179–6182. [DOI] [PMID: 24739148]
[EC 2.1.1.314 created 2015]
 
 
EC 2.4.2.31     
Accepted name: NAD+—protein-arginine ADP-ribosyltransferase
Reaction: NAD+ + protein L-arginine = nicotinamide + Nω-(ADP-D-ribosyl)-protein-L-arginine
Other name(s): ADP-ribosyltransferase; mono(ADP-ribosyl)transferase; NAD+:L-arginine ADP-D-ribosyltransferase; NAD(P)+-arginine ADP-ribosyltransferase; NAD(P)+:L-arginine ADP-D-ribosyltransferase; mono-ADP-ribosyltransferase; ART; ART1; ART2; ART3; ART4; ART5; ART6; ART7; NAD(P)+—protein-arginine ADP-ribosyltransferase; NAD(P)+:protein-L-arginine ADP-D-ribosyltransferase
Systematic name: NAD+:protein-L-arginine ADP-D-ribosyltransferase
Comments: Protein mono-ADP-ribosylation is a reversible post-translational modification that plays a role in the regulation of cellular activities [4]. Arginine residues in proteins act as acceptors. Free arginine, agmatine [(4-aminobutyl)guanidine], arginine methyl ester and guanidine can also do so. The enzyme from some, but not all, species can also use NADP+ as acceptor (giving rise to Nω-[(2′-phospho-ADP)-D-ribosyl]-protein-L-arginine as the product), but more slowly [1,5]. The enzyme catalyses the NAD+-dependent activation of EC 4.6.1.1, adenylate cyclase. Some bacterial enterotoxins possess similar enzymic activities. (cf. EC 2.4.2.36 NAD+diphthamide ADP-ribosyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 81457-93-4
References:
1.  Moss, J., Stanley, S.J. and Oppenheimer, N.J. Substrate specificity and partial purification of a stereospecific NAD- and guanidine-dependent ADP-ribosyltransferase from avian erythrocytes. J. Biol. Chem. 254 (1979) 8891–8894. [PMID: 225315]
2.  Moss, J., Stanley, S.J. and Watkins, P.A. Isolation and properties of an NAD- and guanidine-dependent ADP-ribosyltransferase from turkey erythrocytes. J. Biol. Chem. 255 (1980) 5838–5840. [PMID: 6247348]
3.  Ueda, K. and Hayaishi, O. ADP-ribosylation. Annu. Rev. Biochem. 54 (1985) 73–100. [DOI] [PMID: 3927821]
4.  Corda, D. and Di Girolamo, M. Functional aspects of protein mono-ADP-ribosylation. EMBO J. 22 (2003) 1953–1958. [DOI] [PMID: 12727863]
5.  Paone, G., Stevens, L.A., Levine, R.L., Bourgeois, C., Steagall, W.K., Gochuico, B.R. and Moss, J. ADP-ribosyltransferase-specific modification of human neutrophil peptide-1. J. Biol. Chem. 281 (2006) 17054–17060. [DOI] [PMID: 16627471]
[EC 2.4.2.31 created 1984, modified 1990, modified 2006]
 
 
EC 2.4.2.36     
Accepted name: NAD+diphthamide ADP-ribosyltransferase
Reaction: NAD+ + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Glossary: diphthamide = 2-[4-amino-4-oxo-3-(trimethylammonio)butyl]-L-histidine
Other name(s): ADP-ribosyltransferase; mono(ADPribosyl)transferase; NAD—diphthamide ADP-ribosyltransferase; NAD+:peptide-diphthamide N-(ADP-D-ribosyl)transferase
Systematic name: NAD+:diphthamide-[translation elongation factor 2] N-(ADP-D-ribosyl)transferase
Comments: Diphtheria toxin and some other bacterial toxins catalyse this reaction, which inactivates translation elongation factor 2 (EF2). The acceptor is diphthamide, a unique modification of a histidine residue in the elongation factor found in archaebacteria and all eukaryotes, but not in eubacteria. cf. EC 2.4.2.31 NAD(P)+—protein-arginine ADP-ribosyltransferase. The relevant histidine of EF2 is His715 in mammals, His699 in yeast and His600 in Pyrococcus horikoshii.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 52933-21-8
References:
1.  Lee, H. and Iglewski, W.J. Cellular ADP-ribosyltransferase with the same mechanism of action as diphtheria toxin and Pseudomonas toxin A. Proc. Natl. Acad. Sci. USA 81 (1984) 2703–2707. [DOI] [PMID: 6326138]
2.  Ueda, K. and Hayaishi, O. ADP-ribosylation. Annu. Rev. Biochem. 54 (1985) 73–100. [DOI] [PMID: 3927821]
[EC 2.4.2.36 created 1990, modified 2013]
 
 
EC 2.5.1.108     
Accepted name: 2-(3-amino-3-carboxypropyl)histidine synthase
Reaction: S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2] = S-methyl-5′-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Other name(s): Dph2
Systematic name: S-adenosyl-L-methionine:L-histidine-[translation elongation factor 2] 2-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: A [4Fe-4S] enzyme that modifies a histidine residue of the translation elongation factor 2 (EF2) via a 3-amino-3-carboxypropyl radical. The enzyme is present in archae and eukaryotes but not in eubacteria. The enzyme is a member of the ’AdoMet radical’ (radical SAM) family and generates the 3-amino-3-carboxypropyl radical by an uncanonical clevage of S-adenosyl-L-methionine. The relevant histidine of EF2 is His715 in mammals, His699 in yeast and His600 in Pyrococcus horikoshii. Part of diphthamide biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Liu, S., Milne, G.T., Kuremsky, J.G., Fink, G.R. and Leppla, S.H. Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Mol. Cell Biol. 24 (2004) 9487–9497. [DOI] [PMID: 15485916]
2.  Zhang, Y., Zhu, X., Torelli, A.T., Lee, M., Dzikovski, B., Koralewski, R.M., Wang, E., Freed, J., Krebs, C., Ealick, S.E. and Lin, H. Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature 465 (2010) 891–896. [DOI] [PMID: 20559380]
3.  Zhu, X., Dzikovski, B., Su, X., Torelli, A.T., Zhang, Y., Ealick, S.E., Freed, J.H. and Lin, H. Mechanistic understanding of Pyrococcus horikoshii Dph2, a [4Fe-4S] enzyme required for diphthamide biosynthesis. Mol. Biosyst. 7 (2011) 74–81. [DOI] [PMID: 20931132]
4.  Dong, M., Horitani, M., Dzikovski, B., Pandelia, M.E., Krebs, C., Freed, J.H., Hoffman, B.M. and Lin, H. Organometallic complex formed by an unconventional radical S-adenosylmethionine enzyme. J. Am. Chem. Soc. 138 (2016) 9755–9758. [DOI] [PMID: 27465315]
[EC 2.5.1.108 created 2013]
 
 
EC 3.1.1.97     
Accepted name: methylated diphthine methylhydrolase
Reaction: diphthine methyl ester-[translation elongation factor 2] + H2O = diphthine-[translation elongation factor 2] + methanol
For diagram of diphthamide biosynthesis, click here
Glossary: diphthine methyl ester = 2-[(3S)-3-carboxy methyl ester-3-(trimethylammonio)propyl]-L-histidine
diphthine = 2-[(3S)-3-carboxy-3-(trimethylammonio)propyl]-L-histidine
Other name(s): Dph7; diphthine methylesterase (incorrect)
Systematic name: diphthine methyl ester acylhydrolase
Comments: The protein is only present in eukaryotes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lin, Z., Su, X., Chen, W., Ci, B., Zhang, S. and Lin, H. Dph7 catalyzes a previously unknown demethylation step in diphthamide biosynthesis. J. Am. Chem. Soc. 136 (2014) 6179–6182. [DOI] [PMID: 24739148]
[EC 3.1.1.97 created 2014, modified 2015]
 
 
EC 6.3.1.14     
Accepted name: diphthine—ammonia ligase
Reaction: ATP + diphthine-[translation elongation factor 2] + NH3 = AMP + diphosphate + diphthamide-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Glossary: translation elongation factor 2 = EF2 = eEF2
diphthine = 2-[(3S)-3-carboxy-3-(trimethylammonio)propyl]-L-histidine
diphthamide =2-[(3S)-3-carbamoyl-3-(trimethylammonio)propyl]-L-histidine
Other name(s): diphthamide synthase; diphthamide synthetase; DPH6 (gene name); ATPBD4 (gene name); diphthine:ammonia ligase (AMP-forming)
Systematic name: diphthine-[translation elongation factor 2]:ammonia ligase (AMP-forming)
Comments: This amidase catalyses the last step in the conversion of an L-histidine residue in the translation elongation factor EF2 to diphthamide. This factor is found in all archaea and eukaryota, but not in eubacteria, and is the target of bacterial toxins such as the diphtheria toxin and the Pseudomonas exotoxin A (see EC 2.4.2.36, NAD+diphthamide ADP-ribosyltransferase). The substrate of the enzyme, diphthine, is produced by EC 2.1.1.98, diphthine synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 114514-33-9
References:
1.  Moehring, T.J. and Moehring, J.M. Mutant cultured cells used to study the synthesis of diphthamide. UCLA Symp. Mol. Cell. Biol. New Ser. 45 (1987) 53–63.
2.  Moehring, J.M. and Moehring, T.J. The post-translational trimethylation of diphthamide studied in vitro. J. Biol. Chem. 263 (1988) 3840–3844. [PMID: 3346227]
3.  Su, X., Lin, Z., Chen, W., Jiang, H., Zhang, S. and Lin, H. Chemogenomic approach identified yeast YLR143W as diphthamide synthetase. Proc. Natl. Acad. Sci. USA 109 (2012) 19983–19987. [DOI] [PMID: 23169644]
[EC 6.3.1.14 created 1990 as EC 6.3.2.22, transferred 2010 to EC 6.3.1.14, modified 2013]
 
 
EC 6.3.2.22      
Transferred entry: diphthine—ammonia ligase. Now EC 6.3.1.14, diphthine—ammonia ligase.
[EC 6.3.2.22 created 1990, deleted 2010]
 
 


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