BRENDA - Enzyme Database
show all sequences of 2.5.1.108

Mechanistic understanding of Pyrococcus horikoshii Dph2, a [4Fe-4S] enzyme required for diphthamide biosynthesis

Zhu, X.; Dzikovski, B.; Su, X.; Torelli, A.; Zhang, Y.; Ealick, S.; Freed, J.; Lin, H.; Mol. Biosyst. 7, 74-81 (2011) View publication on PubMedView publication on EuropePMC

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
-
Pyrococcus horikoshii
Crystallization (Commentary)
Crystallization (Commentary)
Organism
-
Pyrococcus horikoshii
Engineering
Protein Variants
Commentary
Organism
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
Pyrococcus horikoshii
C163A
mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
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
Pyrococcus horikoshii
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
Pyrococcus horikoshii
C287A
mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
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
Pyrococcus horikoshii
C59A
mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
C59A/C287A
inactive mutant lacks the Fe-S cluster. A heterodimer of wild-type subunit and C59A/C287A mutant subunit is stable and active
Pyrococcus horikoshii
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Iron-sulfur cluster
each monomer contains three conserved cysteine residues that can bind a [4Fe-4S] cluster. In the reduced state, the [4Fe-4S] cluster can provide one electron to reductively cleave the bound S-adenosyl-L-methionine molecule. The chemistry requires only one [4Fe-4S] cluster to be present in the Dph2 dimer although each monomer can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
Iron-sulfur cluster
each monomer of the dimeric enzyme contains three conserved cysteine residues that can bind a [4Fe–4S] cluster. In the reduced state, the [4Fe–4S] cluster can provide one electron to reductively cleave the bound S-adenosyl-L-methionine molecule
Pyrococcus horikoshii
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
34000
-
2 * 34000, SDS-PAGE
Pyrococcus horikoshii
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
Pyrococcus horikoshii
first step of diphthamide biosynthesis, a unique posttranslational modification on a histidine residue of translational elongation factor 2
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
Pyrococcus horikoshii
the enzyme is involved in diphthamide biosynthesis
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Pyrococcus horikoshii
O58832
-
-
Purification (Commentary)
Purification (Commentary)
Organism
-
Pyrococcus horikoshii
wild-type and mutant enzymes
Pyrococcus horikoshii
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
-
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
-
-
-
?
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
first step of diphthamide biosynthesis, a unique posttranslational modification on a histidine residue of translational elongation factor 2
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
-
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
the enzyme is involved in diphthamide biosynthesis
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
-
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
the 3-amino-3-carboxypropyl radical is added to the imidazole ring in the pathway towards the formation of the product
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
-
-
-
?
Subunits
Subunits
Commentary
Organism
homodimer
-
Pyrococcus horikoshii
homodimer
2 * 34000, SDS-PAGE
Pyrococcus horikoshii
Synonyms
Synonyms
Commentary
Organism
PhDph2
-
Pyrococcus horikoshii
S-adenosyl-L-methionine:L-histidine 3-amino-3-carboxypropyltransferase
-
Pyrococcus horikoshii
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
65
-
assay at
Pyrococcus horikoshii
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Pyrococcus horikoshii
Cloned(Commentary) (protein specific)
Commentary
Organism
-
Pyrococcus horikoshii
Crystallization (Commentary) (protein specific)
Crystallization
Organism
-
Pyrococcus horikoshii
Engineering (protein specific)
Protein Variants
Commentary
Organism
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
Pyrococcus horikoshii
C163A
mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
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
Pyrococcus horikoshii
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
Pyrococcus horikoshii
C287A
mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
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
Pyrococcus horikoshii
C59A
mutant enzyme has lower activity than wild-type enzyme and can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
C59A/C287A
inactive mutant lacks the Fe-S cluster. A heterodimer of wild-type subunit and C59A/C287A mutant subunit is stable and active
Pyrococcus horikoshii
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Iron-sulfur cluster
each monomer contains three conserved cysteine residues that can bind a [4Fe-4S] cluster. In the reduced state, the [4Fe-4S] cluster can provide one electron to reductively cleave the bound S-adenosyl-L-methionine molecule. The chemistry requires only one [4Fe-4S] cluster to be present in the Dph2 dimer although each monomer can bind a [4Fe-4S] cluster
Pyrococcus horikoshii
Iron-sulfur cluster
each monomer of the dimeric enzyme contains three conserved cysteine residues that can bind a [4Fe–4S] cluster. In the reduced state, the [4Fe–4S] cluster can provide one electron to reductively cleave the bound S-adenosyl-L-methionine molecule
Pyrococcus horikoshii
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
34000
-
2 * 34000, SDS-PAGE
Pyrococcus horikoshii
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
Pyrococcus horikoshii
first step of diphthamide biosynthesis, a unique posttranslational modification on a histidine residue of translational elongation factor 2
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
Pyrococcus horikoshii
the enzyme is involved in diphthamide biosynthesis
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
-
Pyrococcus horikoshii
wild-type and mutant enzymes
Pyrococcus horikoshii
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
-
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
-
-
-
?
S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2]
first step of diphthamide biosynthesis, a unique posttranslational modification on a histidine residue of translational elongation factor 2
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
-
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
the enzyme is involved in diphthamide biosynthesis
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
-
-
-
?
S-adenosyl-L-methionine + L-histidine600-[translation elongation factor 2]
the 3-amino-3-carboxypropyl radical is added to the imidazole ring in the pathway towards the formation of the product
723158
Pyrococcus horikoshii
S-methyl-5'-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine600-[translation elongation factor 2]
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homodimer
-
Pyrococcus horikoshii
homodimer
2 * 34000, SDS-PAGE
Pyrococcus horikoshii
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
65
-
assay at
Pyrococcus horikoshii
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Pyrococcus horikoshii
General Information
General Information
Commentary
Organism
physiological function
first step of diphthamide biosynthesis, a unique posttranslational modification on a histidine residue of translational elongation factor 2
Pyrococcus horikoshii
General Information (protein specific)
General Information
Commentary
Organism
physiological function
first step of diphthamide biosynthesis, a unique posttranslational modification on a histidine residue of translational elongation factor 2
Pyrococcus horikoshii
Other publictions for EC 2.5.1.108
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
758825
Fenwick
The crystal structure of Dph2 ...
Methanobrevibacter smithii, Methanobrevibacter smithii DSM 861
Biochemistry
58
4343-4351
2019
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-
1
1
-
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-
-
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2
-
2
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1
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2
1
2
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1
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1
1
1
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2
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1
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2
1
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759511
Dong
The asymmetric function of Dp ...
Saccharomyces cerevisiae
J. Biol. Inorg. Chem.
24
777-782
2019
-
-
-
-
4
-
-
-
-
-
-
1
-
5
-
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-
-
-
-
-
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2
1
1
-
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1
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1
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4
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1
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2
1
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-
-
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759725
Dong
Methods for studying the radi ...
Saccharomyces cerevisiae, Pyrococcus horikoshii, Saccharomyces cerevisiae BY4741
Methods Enzymol.
606
421-438
2018
-
-
2
-
-
-
-
-
-
-
-
3
-
72
-
-
2
-
-
-
-
-
3
2
3
-
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-
-
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-
2
-
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-
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-
2
2
-
-
-
-
-
-
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-
3
-
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-
2
-
-
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3
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
759402
Dong
Substrate-dependent cleavage ...
Pyrococcus horikoshii
J. Am. Chem. Soc.
139
5680-5683
2017
-
-
-
-
-
-
-
-
-
-
-
3
-
1
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3
1
1
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1
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1
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3
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3
1
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-
-
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-
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738461
Dong
An organometallic complex form ...
Pyrococcus horikoshii
J. Am. Chem. Soc.
138
9755-9758
2016
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-
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-
-
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2
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2
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1
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1
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1
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2
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-
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-
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-
739730
Abdel-Fattah
Insights into diphthamide, key ...
Saccharomyces cerevisiae
Toxins
5
958-968
2013
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-
1
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-
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1
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1
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1
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-
-
-
-
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1
1
-
-
-
723158
Zhu
Mechanistic understanding of P ...
Pyrococcus horikoshii
Mol. Biosyst.
7
74-81
2011
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1
1
8
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-
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-
2
1
2
-
4
-
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2
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-
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4
2
2
1
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1
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1
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1
8
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2
1
2
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2
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4
2
1
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1
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1
1
-
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723263
Zhang
Lin, H.: Diphthamide biosynthe ...
Pyrococcus horikoshii
Nature
465
891-896
2010
-
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2
2
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-
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2
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2
-
1
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1
1
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3
1
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2
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2
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2
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2
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1
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3
1
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1
1
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725594
Webb
Diphthamide modification of eE ...
Mus musculus
J. Cell Sci.
121
3140-3145
2008
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1
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1
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1
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1
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1
1
-
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718109
Liu
Identification of the proteins ...
Saccharomyces cerevisiae, Mus musculus
Mol. Cell. Biol.
24
9487-9497
2004
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2
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2
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4
4
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725093
Mattheakis
Diphthamide synthesis in Sacch ...
Saccharomyces cerevisiae, Saccharomyces cerevisiae FY251
Gene
132
149-154
1993
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1
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2
2
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2
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2
2
2
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1
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1
1
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2
2
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2
2
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