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show all sequences of 2.8.1.4

Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis

Liu, Y.; Zhu, X.; Nakamura, A.; Orlando, R.; Soell, D.; Whitman, W.B.; J. Biol. Chem. 287, 36683-36692 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
-
Methanococcus maripaludis
Engineering
Amino acid exchange
Commentary
Organism
C265A
cells expressing the C265A variant show 88% decrease in their 4-thiouridine level. The mutant enzyme contains no detectable amount of persulfide
Methanococcus maripaludis
C268A
cells expressing the C265A variant contain no 4-thiouridine. The mutant enzyme contains no detectable amount of persulfide
Methanococcus maripaludis
C348A
cells expressing the C348A variant show 33% decreases in their 4-thiouridine levels. The mutant enzyme contains no detectable amount of persulfide
Methanococcus maripaludis
C78A
cells expressing the C78A variant show 8% decrease in their 4-thiouridine levels. The C78A variant has similar amounts of persulfide as the wild-type protein
Methanococcus maripaludis
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1
-
Sulfide
pH 7.3, 37°C
Methanococcus maripaludis
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
additional information
no spectroscopic features indicative of Fe-S clusters are present
Methanococcus maripaludis
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
sulfide + tRNA-uridine
Methanococcus maripaludis
the enzyme is invoved in biosynthesis of 4-thiouridine in tRNA. 4-Thiouridine, is a modified nucleotide of tRNA that is conserved from bacteria to archaea, where it functions as a sensor for near-UV irradiation
tRNA-4-thiouridine
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Methanococcus maripaludis
Q6LXJ6
-
-
Purification (Commentary)
Commentary
Organism
-
Methanococcus maripaludis
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
sulfide + tRNA-uridine
the enzyme is invoved in biosynthesis of 4-thiouridine in tRNA. 4-Thiouridine, is a modified nucleotide of tRNA that is conserved from bacteria to archaea, where it functions as a sensor for near-UV irradiation
725494
Methanococcus maripaludis
tRNA-4-thiouridine
-
-
-
?
sulfide + [tRNACys]-uridine
proposed mechanism: first, a sulfur donor (equivalent of S2-) attacks the Cys265–Cys268 disulfide linkage to generate a persulfide on either Cys265 or Cys268, leaving the other Cys as a free thiol. Then, a thiolate derived from deprotonation of the free thiol attacks the bridging sulfur of the persulfide to liberate the terminal sulfur. After donation of the sulfur (in the -2 oxidation state) to form 4-thiouridine, the disulfide (with both sulfurs in the -1 oxidation state) is consequently regenerated. No exogenous electron donor or acceptor is required for the catalytic cycle
725494
Methanococcus maripaludis
[tRNACys]-4-thiouridine
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Methanococcus maripaludis
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.3
-
assay at
Methanococcus maripaludis
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
the enzyme requires two conserved Cys residues (Cys265 and Cys268), which are arranged in a CXXC motif in the PP-loop domain, for both in vitro and in vivo activities to generate 4-thiouridine in tRNAs
Methanococcus maripaludis
Cloned(Commentary) (protein specific)
Commentary
Organism
-
Methanococcus maripaludis
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
additional information
the enzyme requires two conserved Cys residues (Cys265 and Cys268), which are arranged in a CXXC motif in the PP-loop domain, for both in vitro and in vivo activities to generate 4-thiouridine in tRNAs
Methanococcus maripaludis
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
C265A
cells expressing the C265A variant show 88% decrease in their 4-thiouridine level. The mutant enzyme contains no detectable amount of persulfide
Methanococcus maripaludis
C268A
cells expressing the C265A variant contain no 4-thiouridine. The mutant enzyme contains no detectable amount of persulfide
Methanococcus maripaludis
C348A
cells expressing the C348A variant show 33% decreases in their 4-thiouridine levels. The mutant enzyme contains no detectable amount of persulfide
Methanococcus maripaludis
C78A
cells expressing the C78A variant show 8% decrease in their 4-thiouridine levels. The C78A variant has similar amounts of persulfide as the wild-type protein
Methanococcus maripaludis
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1
-
Sulfide
pH 7.3, 37°C
Methanococcus maripaludis
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
additional information
no spectroscopic features indicative of Fe-S clusters are present
Methanococcus maripaludis
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
sulfide + tRNA-uridine
Methanococcus maripaludis
the enzyme is invoved in biosynthesis of 4-thiouridine in tRNA. 4-Thiouridine, is a modified nucleotide of tRNA that is conserved from bacteria to archaea, where it functions as a sensor for near-UV irradiation
tRNA-4-thiouridine
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
-
Methanococcus maripaludis
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
sulfide + tRNA-uridine
the enzyme is invoved in biosynthesis of 4-thiouridine in tRNA. 4-Thiouridine, is a modified nucleotide of tRNA that is conserved from bacteria to archaea, where it functions as a sensor for near-UV irradiation
725494
Methanococcus maripaludis
tRNA-4-thiouridine
-
-
-
?
sulfide + [tRNACys]-uridine
proposed mechanism: first, a sulfur donor (equivalent of S2-) attacks the Cys265–Cys268 disulfide linkage to generate a persulfide on either Cys265 or Cys268, leaving the other Cys as a free thiol. Then, a thiolate derived from deprotonation of the free thiol attacks the bridging sulfur of the persulfide to liberate the terminal sulfur. After donation of the sulfur (in the -2 oxidation state) to form 4-thiouridine, the disulfide (with both sulfurs in the -1 oxidation state) is consequently regenerated. No exogenous electron donor or acceptor is required for the catalytic cycle
725494
Methanococcus maripaludis
[tRNACys]-4-thiouridine
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Methanococcus maripaludis
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.3
-
assay at
Methanococcus maripaludis
General Information
General Information
Commentary
Organism
malfunction
deletion mutant shows no groth defects compared to wild-type, indicating that MMP1354 is not an essential enzyme; deletion of ThiI abolishes the biosynthesis of 4-thiouridine but not of thiamine; MMP1354 complements an Escherichia coli Thi mutant
Methanococcus maripaludis
General Information (protein specific)
General Information
Commentary
Organism
malfunction
deletion mutant shows no groth defects compared to wild-type, indicating that MMP1354 is not an essential enzyme; deletion of ThiI abolishes the biosynthesis of 4-thiouridine but not of thiamine; MMP1354 complements an Escherichia coli Thi mutant
Methanococcus maripaludis
Other publictions for EC 2.8.1.4
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
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)
725494
Liu
Biosynthesis of 4-thiouridine ...
Methanococcus maripaludis
J. Biol. Chem.
287
36683-36692
2012
-
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1
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4
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1
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1
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1
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6
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1
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2
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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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4
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1
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1
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1
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-
-
1
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-
-
-
2
-
1
-
-
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1
-
-
-
-
1
1
-
-
-
694891
Dewez
The conserved wobble uridine t ...
Caenorhabditis elegans, Schizosaccharomyces pombe
Proc. Natl. Acad. Sci. USA
105
5459-5464
2008
-
-
-
-
2
-
-
-
-
-
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4
-
4
-
-
-
-
-
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-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
4
-
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-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
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-
676149
Numata
Snapshots of tRNA sulphuration ...
Escherichia coli
Nature
442
419-424
2006
-
-
-
1
-
-
-
-
-
-
-
-
-
1
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-
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1
-
-
-
-
-
-
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-
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-
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-
-
-
-
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-
1
-
-
-
-
-
-
-
-
-
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-
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-
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
643812
Harris
Mammalian tRNA sulfurtransfera ...
Rattus norvegicus
Nucleic Acids Res.
5
599-613
1978
-
-
-
-
-
-
1
-
-
1
-
1
-
2
-
-
-
-
-
9
-
1
7
-
-
1
-
-
1
1
1
1
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
1
-
1
-
-
-
-
-
9
-
1
7
-
-
1
-
-
1
1
1
-
-
-
-
-
-
-
643811
Harris
tRNA sulfurtransferase: a memb ...
Rattus norvegicus
Biochem. Biophys. Res. Commun.
79
657-662
1977
-
-
-
-
-
-
-
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-
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1
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1
1
3
2
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1
1
3
2
-
-
-
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643809
Thimmappaya
-
Studies on transfer ribonuclei ...
Pseudomonas aeruginosa
Indian J. Biochem. Biophys.
12
405-407
1975
-
-
-
-
-
-
-
-
-
1
-
1
-
1
-
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1
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-
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2
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1
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2
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2
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1
-
1
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-
-
1
-
-
-
-
2
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
643810
Wong
The presence of an inhibitor o ...
Rattus norvegicus
Biochem. Biophys. Res. Commun.
65
1137-1145
1975
-
-
-
-
-
-
1
-
1
1
-
1
-
1
-
-
-
-
-
2
-
1
2
-
-
-
-
-
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1
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1
-
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-
-
1
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1
1
-
1
-
-
-
-
-
2
-
1
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
643808
Wong
Transfer ribonucleic acid sulf ...
Rattus norvegicus
Biochemistry
13
2805-2812
1974
1
-
-
-
-
-
1
-
1
1
-
1
-
1
-
-
1
-
-
1
1
1
7
-
-
-
-
-
1
1
-
2
-
-
-
1
-
-
2
-
-
-
-
1
-
-
1
1
-
1
-
-
-
1
-
1
1
1
7
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
643806
Abrell
The biosynthesis of 4-thiourid ...
Escherichia coli, Escherichia coli B / ATCC 11303
J. Biol. Chem.
246
294-301
1971
-
-
-
-
-
-
5
1
-
1
-
2
-
177
-
-
1
-
-
-
-
2
12
-
-
-
-
-
1
-
-
2
-
-
-
-
-
-
2
-
-
-
-
5
-
1
-
1
-
2
-
-
-
1
-
-
-
2
12
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
643807
Harris
Sulfur-deficient transfer ribo ...
Escherichia coli, Escherichia coli HfrC
Biochemistry
10
4207-4212
1971
-
-
-
-
-
-
-
2
-
1
-
2
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2
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8
-
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1
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1
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2
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1
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2
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8
-
-
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-
-
-
-
-
-
-
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-
-
-
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643805
Wong
Ribonucleic acid sulfurtransfe ...
Bacillus subtilis, Bacillus subtilis W168
Biochemistry
9
2376-2386
1970
-
-
-
-
-
-
1
2
-
1
-
2
-
4
-
-
1
-
-
-
1
-
13
-
-
-
-
-
-
-
-
1
1
-
-
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-
1
-
-
-
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1
1
2
-
1
-
2
-
-
-
1
-
-
1
-
13
-
-
-
-
-
-
-
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-
-
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-
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