show all | hide all No of entries

Information on EC 2.5.1.108 - 2-(3-amino-3-carboxypropyl)histidine synthase and Organism(s) Pyrococcus horikoshii and UniProt Accession O58832

for references in articles please use BRENDA:EC2.5.1.108
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
IUBMB 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.
Specify your search results
Select one or more organisms in this record:
This record set is specific for:
Pyrococcus horikoshii
UNIPROT: O58832
The expected taxonomic range for this enzyme is: Eukaryota, Archaea
The taxonomic range for the selected organisms is: Pyrococcus horikoshii
Synonyms
diphthine synthase, Dph2, DPH4, PhDph2, S-adenosyl-L-methionine:L-histidine 3-amino-3-carboxypropyltransferase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PhDph2
298649
-
S-adenosyl-L-methionine:L-histidine 3-amino-3-carboxypropyltransferase
298649
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
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]
show the reaction diagram
unlike the enzymes in the radical S-adenosyl-L-methionine superfamily, Dph2 does not form the canonical 5'-deoxyadenosyl radical. Instead, it breaks the Cgamma,Met-S bond of S-adenosyl-L-methionine and generates a 3-amino-3-carboxylpropyl radical
-
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:L-histidine-[translation elongation factor 2] 2-[(3S)-3-amino-3-carboxypropyl]transferase
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.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
L-histidine-[translation elongation factor 2] + S-adenosyl-L-methionine
2-((3S)-3-amino-3-carboxypropyl)-L-histidine-[translation elongation factor 2] + S-methyl-5'-thioadenosine
show the reaction diagram
-
-
-
-
?
L-histidine-[translation elongation factor 2] + [[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl][(2E)-3-carboxyprop-2-en-1-yl]methylsulfonium
2-(3-carboxyprop-2-en-1-yl)-L-histidine-[translation elongation factor 2] + S-methyl-5'-thioadenosine
show the reaction diagram
-
S-adenosyl-L-methionine analogue, in which the 3-amino-3-carboxypropyl group is replaced with a 3-carboxyallyl group. The analogue is cleaved by Dph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, alpha-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Data support a pi-complex between the C=C double bond of alpha-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster, i.e. a radical S-adenosyl-L-methionine-related [4Fe-4S]+ cluster forming an organometallic complex with an alkene
-
-
?
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]
show the reaction diagram
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-carboxypropyl]-L-histidine-[translation elongation factor 2]
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine500-[translation elongation factor 2]
show the reaction diagram
-
the enzyme is involved in diphthamide biosynthesis
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
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]
show the reaction diagram
O58832
first step of diphthamide biosynthesis, a unique posttranslational modification on a histidine residue of translational elongation factor 2
-
-
?
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-carboxypropyl]-L-histidine-[translation elongation factor 2]
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine500-[translation elongation factor 2]
show the reaction diagram
-
the enzyme is involved in diphthamide biosynthesis
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
show the reaction diagram
O58832
the enzyme is involved in diphthamide biosynthesis
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
[4Fe-4S]-center
-
cleavage of a S-adenosyl-L-methionine analogue, in which the 3-amino-3-carboxypropyl group is replaced with a 3-carboxyallyl group, yields a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, alpha-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Data support a pi-complex between the C=C double bond of alpha-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster, i.e. a radical S-adenosyl-L-methionine-related [4Fe-4S]+ cluster forming an organometallic complex with an alkene
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
-
a [4Fe–4S] enzyme
Iron-sulfur cluster
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
34000
-
2 * 34000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
crystal structure at 2.3 A resolution; hanging-drop vapour-diffusionmethod, X-ray crystal structure at 2.3 A resolution using selenomethionine single-wavelength anomalous diffraction phasing
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C163A
-
difference in the EPR spectrum of the reduced form, pronounced rhombic main features with greatly increased g-value anisotropy, mutant enzyme is able to transfer the the 3-amino-3-carboxypropyl group onto His600; mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
C259A/C287A
-
homodimeric mutant enzyme not stable. It is inactive and cannot bind a [4Fe-4S] cluster. Heterodimeric enzyme with a wild-type subunit and a mutant subunit is active
C287A
-
difference in the EPR spectrum, g-tensors are more axial than wild type, mutant enzyme is able to transfer the the 3-amino-3-carboxypropyl group onto His600; mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
C59A
-
difference in the EPR spectrum, g-tensors are more axial than wild type, mutant enzyme is able to transfer the the 3-amino-3-carboxypropyl group onto His600; mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
C59A/C287A
-
inactive mutant lacks the Fe-S cluster. A heterodimer of wild-type subunit and C59A/C287A mutant subunit is stable and active
PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
; wild-type and mutant enzymes
-
CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli; expression in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Zhu, X.; Dzikovski, B.; Su, X.; Torelli, A.; Zhang, Y.; Ealick, S.; Freed, J.; Lin, H.
Mechanistic understanding of Pyrococcus horikoshii Dph2, a [4Fe-4S] enzyme required for diphthamide biosynthesis
Mol. Biosyst.
7
74-81
2011
Pyrococcus horikoshii (O58832), Pyrococcus horikoshii
Manually annotated by BRENDA team
Zhang, Y.; Zhu, X.; Torelli, A.T.; Lee, M.; Dzikovski, B.; Koralewski, R.M.; Wang, E.; Freed, J.; Krebs, C.; Ealick, S.E.
Lin, H.: Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme
Nature
465
891-896
2010
Pyrococcus horikoshii (O58832)
Manually annotated by BRENDA team
Dong, M.; Horitani, M.; Dzikovski, B.; Pandelia, M.E.; Krebs, C.; Freed, J.H.; Hoffman, B.M.; Lin, H.
An organometallic complex formed by an unconventional radical SAM enzyme
J. Am. Chem. Soc.
138
9755-9758
2016
Pyrococcus horikoshii (O58832), Pyrococcus horikoshii
Manually annotated by BRENDA team
Select items on the left to see more content.