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Information on EC 2.1.1.98 - diphthine synthase
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2.1.1.98 diphthine synthaseIUBMB 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.
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Word Map
- 2.1.1.98
- diphthamide
- toxin
-
pyrococcus
- horikoshii
-
trimethylation
-
diphtheria
- eef2
-
ill-defined
-
eukaryal
- amidase
The expected taxonomic range for this enzyme is: Archaea, Bacteria, Eukaryota
Reaction Schemes
3
+
=
3
+
3
+
=
3
+
diphthine-[translation elongation factor 2]
Synonyms
diphthine synthase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
diphthine methyltransferase
-
-
-
-
diphthine synthase
Dph5
methyltransferase, diphthine
-
-
-
-
S-adenosyl-L-methionine:elongation factor 2 methyltransferase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
-
-
-
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]
(1c)
-
-
-
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]
(1b)
-
-
-
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]
(1a)
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
methyl group transfer
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
-
-
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine-[translation elongation factor 2]-forming)
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.
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CAS REGISTRY NUMBER
COMMENTARY
114514-25-9
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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]
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]
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]
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]
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]
the enzyme acts on His600 of elongation factor 2. It is involved in diphthamide biosynthesis
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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]
the enzyme acts on His600 of elongation factor 2. It is involved in diphthamide biosynthesis
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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]
-
-
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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]
-
-
-
-
?
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]
-
-
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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]
the enzyme catalyzes the trimethylation in a highly processive manner. It acts on His600 of elongation factor 2. Mono- and dimethylated PhEF2 are detected, while the trimethylated product cannot be detected due to the facile elimination of the trimethylamino group
-
-
?
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]
-
-
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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]
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]
-
-
-
-
?
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]
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]
-
-
-
-
?
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]
the enzyme acts on His600 of elongation factor 2. It is involved in diphthamide biosynthesis
-
-
?
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]
the enzyme acts on His600 of elongation factor 2. It is involved in diphthamide biosynthesis
-
-
?
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
-
-
?
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]
-
-
-
-
?
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]
-
-
-
-
?
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
metabolism
-
the enzyme carries out the second step of diphthamide synthesis
metabolism
-
the enzyme carries out the second step of diphthamide synthesis
-
physiological function
the enzyme is involved in diphthamide biosynthesis
physiological function
-
the enzyme is involved in diphthamide biosynthesis
-
Show AA Sequence and Transmembrane Helices (2266 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
29600
2 * 29600, calculated from sequence, crystallographic data, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine, while the other active site contains no ligand
31500
2 * 31500, calculated from sequence, crystallographic data, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine, while the other active site contains no ligand
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
dimer
2 * 31500, calculated from sequence, crystallographic data, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine, while the other active site contains no ligand
dimer
-
2 * 31500, calculated from sequence, crystallographic data, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine, while the other active site contains no ligand
-
dimer
2 * 29600, calculated from sequence, crystallographic data, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine, while the other active site contains no ligand
dimer
-
2 * 29600, calculated from sequence, crystallographic data, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine, while the other active site contains no ligand
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapour-diffusion method at 20°C, structure is resolved at 2.0 A resolution. The homodimeric crystal structures of the archaeal diphthine synthases from Pyrococcus horikoshii DSM 12428 and Aeropyrum pernix DSM 11879 share the same overall fold as the cobalt-precorrin-4 methyltransferase CbiF
microbatch method, structure is resolved at 2.1 A resolution. The homodimeric crystal structures of the archaeal diphthine synthases from Pyrococcus horikoshii DSM 12428 and Aeropyrum pernix DSM 11879share the same overall fold as the cobalt-precorrin-4 methyltransferase CbiF
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
dph7 mutants show drastically upregulated interaction between the enzyme and eukaryal translation elongation factor 2, indicating that their association is kept in check by Dph7
dph7 mutants show drastically upregulated interaction between the enzyme and eukaryal translation elongation factor 2, indicating that their association is kept in check by Dph7
-
dph7 mutants show drastically upregulated interaction between the enzyme and eukaryal translation elongation factor 2, indicating that their association is kept in check by Dph7
-
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kishishita, S.; Shimizu, K.; Murayama, K.; Terada, T.; Shirouzu, M.; Yokoyama, S.; Kunishima, N.
Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2
Acta Crystallogr. Sect. D
64
397-406
2008
Pyrococcus horikoshii (O58456), Pyrococcus horikoshii, Aeropyrum pernix (Q9YDI2), Aeropyrum pernix DSM 11879 (Q9YDI2), Pyrococcus horikoshii DSM 12428 (O58456)
brenda
Zhu, X.; Kim, J.; Su, X.; Lin, H.
Reconstitution of diphthine synthase activity in vitro
Biochemistry
49
9649-9657
2010
Pyrococcus horikoshii (O58456), Pyrococcus horikoshii, Pyrococcus horikoshii DSM 12428 (O58456)
brenda
Uthman, S.; Baer, C.; Scheidt, V.; Liu, S.; ten Have, S.; Giorgini, F.; Stark, M.J.; Schaffrath, R.
The amidation step of diphthamide biosynthesis in yeast requires DPH6, a gene identified through mining the DPH1-DPH5 interaction network
PLoS Genet.
9
e1003334
2013
Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4741
brenda
Lin, Z.; Su, X.; Chen, W.; Ci, B.; Zhang, S.; Lin, H.
Dph7 catalyzes a previously unknown demethylation step in diphthamide biosynthesis
J. Am. Chem. Soc.
136
6179-6182
2014
Saccharomyces cerevisiae
brenda
Hoerberg, J.; Saenz-Mendez, P.; Eriksson, L.A.
QM/MM studies of Dph5 - a promiscuous methyltransferase in the eukaryotic biosynthetic pathway of diphthamide
J. Chem. Inf. Model.
58
1406-1414
2018
Saccharomyces cerevisiae
brenda
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Release 2023.1 (January 2023)
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