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Enzyme Nomenclature
Information on EC 2.8.1.15 - tRNA-5-methyluridine54 2-sulfurtransferase
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EC Tree
2.8.1.15 tRNA-5-methyluridine54 2-sulfurtransferaseIUBMB Comments
The enzyme, found in thermophilic bacteria and archaea, modifies the ribothymidine (5-methyluridine) residue at position 54 of tRNAs. Contains zinc and an [4Fe-4S] cluster. Some organisms, such as the archaeon Pyrococcus horikoshii, do not have a TtuB sulfur-carrier protein, and appear to use sulfide as the sulfur source.
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The expected taxonomic range for this enzyme is: Archaea, Bacteria
Reaction Schemes
+
+
+
=
+
+
+
+
[TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH
+
5-methyluracil54 in tRNA
+
=
+
+
5-methyl-2-thiouracil54 in tRNA
+
[TtuB sulfur-carrier protein]-Gly-Gly
+
+
+
=
+
+
+
+
[TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH
+
5-methyuracil54 in tRNA
+
=
+
+
5-methyl-2-thiouracil54 in tRNA
+
[TtuB sulfur-carrier protein]-Gly-Gly
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PH0300
TTC0106
TtuA
TT_C0106
Veg136 protein
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluracil54 in tRNA + H2O = AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
-
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O = AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
-
-
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SYSTEMATIC NAME
IUBMB Comments
[TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH:tRNA (5-methyluridine54-2-O)-sulfurtransferase
The enzyme, found in thermophilic bacteria and archaea, modifies the ribothymidine (5-methyluridine) residue at position 54 of tRNAs. Contains zinc and an [4Fe-4S] cluster. Some organisms, such as the archaeon Pyrococcus horikoshii, do not have a TtuB sulfur-carrier protein, and appear to use sulfide as the sulfur source.
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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
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 2-thioribothymidine in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 2-thioribothymidine in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 2-thioribothymidine in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 2-thioribothymidine in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 2-thioribothymidine in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
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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
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyluridine54 in tRNA + acceptor
AMP + diphosphate + 5-methyl-2-thiouridine54 in tRNA + [TtuB sulfur-carrier protein] + reduced acceptor
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
ATP + [TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + 5-methyuracil54 in tRNA + H2O
AMP + diphosphate + 5-methyl-2-thiouracil54 in tRNA + [TtuB sulfur-carrier protein]-Gly-Gly
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
[4Fe-4S]-center
TtuA requires oxygen-labile [4Fe-4S]-type iron (Fe)-S clusters for its enzymatic activity. The [4Fe-4S] cluster is coordinated by three highly conserved cysteine residues, and one of the Fe atoms is exposed to the active site. The cluster is coordinated by conserved residues Cys130, Cys133, and Cys222
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zinc
Zinc
TtuA has four conserved CXXC motifs and one CXXH motif. In the TtuA structure, the first zinc finger is made up of the first and second CXXC/H motifs, where the zinc atom is coordinated by Cys3, Cys6, Cys22, and His25. The second zinc finger is made up of the fourth and fifth CXXC motifs, where the zinc atom is coordinated by Cys272, Cys275, Cys284, and Cys287
Zinc
presence of zinc atoms in the protein crystal. TtuA contains five characteristic metal ion-binding motifs, CXXC/H
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50 - 70
thiolation increases 7fold when the temperature rises from 50°C to 70°C
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
brenda
-
SwissProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
metabolism
2-Thioribothymidine (s2T) is a modified nucleoside of U, specifically found at position 54 of tRNAs from extreme thermophilic microorganisms. The function of the 2-thiocarbonyl group of s2T54 is thermostabilization of the three-dimensional structure of tRNA
metabolism
The enzyme is required for growth at temperatures above 75°C. Thiolation of thymidine54 in tRNA results in a tRNA molecule with higher thermostability
metabolism
-
The enzyme is required for growth at temperatures above 75°C. Thiolation of thymidine54 in tRNA results in a tRNA molecule with higher thermostability
-
metabolism
-
2-Thioribothymidine (s2T) is a modified nucleoside of U, specifically found at position 54 of tRNAs from extreme thermophilic microorganisms. The function of the 2-thiocarbonyl group of s2T54 is thermostabilization of the three-dimensional structure of tRNA
-
metabolism
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
2-Thioribothymidine (s2T) is a modified nucleoside of U, specifically found at position 54 of tRNAs from extreme thermophilic microorganisms. The function of the 2-thiocarbonyl group of s2T54 is thermostabilization of the three-dimensional structure of tRNA
-
physiological function
a mutant strain without TtuA activity lacks 2-thioribothymidine in tRNA, exhibits normal growth at an optimal temperature of 7 °C, and shows growth defects at temperatures higher than 80°C
physiological function
mutation of either gene TtuA or TtuB completely abolishes thio-modification of 2-thioribothymidine, and the mutants exhibit a temperature-sensitive phenotype. TtuA is possibly an ATPase possessing a P-loop motif. TtuB is a putative thio-carrier protein. Both TtuA and TtuB are required for 2-thioribothymidine in vitro formation in the presence of cysteine and ATP
physiological function
the sulfur atom of 2-thioribothymidine in tRNA is derived from cysteine or sulfate. Specific 2-thiolation of ribothymidine, at position 54, is observed in vitro, in the presence of ATP. The 2-thiolation reaction in vitro as well as expression of 2-thiolation enzymes in vivo show strong temperature dependence
physiological function
-
the sulfur atom of 2-thioribothymidine in tRNA is derived from cysteine or sulfate. Specific 2-thiolation of ribothymidine, at position 54, is observed in vitro, in the presence of ATP. The 2-thiolation reaction in vitro as well as expression of 2-thiolation enzymes in vivo show strong temperature dependence
-
physiological function
-
a mutant strain without TtuA activity lacks 2-thioribothymidine in tRNA, exhibits normal growth at an optimal temperature of 7 °C, and shows growth defects at temperatures higher than 80°C
-
physiological function
-
mutation of either gene TtuA or TtuB completely abolishes thio-modification of 2-thioribothymidine, and the mutants exhibit a temperature-sensitive phenotype. TtuA is possibly an ATPase possessing a P-loop motif. TtuB is a putative thio-carrier protein. Both TtuA and TtuB are required for 2-thioribothymidine in vitro formation in the presence of cysteine and ATP
-
physiological function
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
the sulfur atom of 2-thioribothymidine in tRNA is derived from cysteine or sulfate. Specific 2-thiolation of ribothymidine, at position 54, is observed in vitro, in the presence of ATP. The 2-thiolation reaction in vitro as well as expression of 2-thiolation enzymes in vivo show strong temperature dependence
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). TTUA_THET2
Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
321
0
36194
Swiss-Prot
-
A0A7R9NCP7_9EURY
301
0
34699
TrEMBL
-
A0A644V5Q8_9ZZZZ
300
0
32759
TrEMBL
other Location (Reliability: 3)
A0A7R9RAN3_9EURY
301
0
34656
TrEMBL
-
A0A644T000_9ZZZZ
302
0
33548
TrEMBL
other Location (Reliability: 3)
TTUA_PYRHO
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
310
0
35633
Swiss-Prot
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method at 208C, using 1 microl of sample solution mixed with an equal volume of reservoir solution, composed of 100 mM BicineNaOH buffer (pH 9.0) containing 200 mM NaCl, 12% (w/v) polyethylene glycol(PEG) 3350, and 010% (v/v) N,N-dimethylformamide. The native crystal belongs to the space group P43212, with unit cell parameters of a 5 b 5 70.1 Angstrom and c 5 128.6 Angstrom
to 2.1 A resolution. TtuA forms a homodimer, and each subunit contains a catalytic domain and unique N- and C-terminal zinc fingers. Three conserved cysteine residues are clustered in the putative catalytic site
structure of the TtuA-TtuB complex, at a resolution of 2.5 A, showing the S transfer of TtuB to tRNA using its C-terminal thiocarboxylate group. The active site of TtuA is connected to the outside by two channels, one occupied by TtuB and the other used for tRNA binding
vapour-diffusion method at 293 K under anaerobic conditions, 2-thioribothymidinesynthetic complex TtuATtuB
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C130S
C133S
C222S
D161A
D59A
E203A
H157A
K58A
N158A
C130S
C133S
C222S
D59A
H157A
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the TtuA-TtuB complex has a strong tendency to aggregate. TtuA is unstable under aerobic conditions but stable under anaerobic conditions.
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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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
enzyme expression increases with increasing the temperature from 50C to 80C
enzyme expression increases with increasing the temperature from 50C to 80C
enzyme expression increases with increasing the temperature from 50C to 80C
-
-
enzyme expression increases with increasing the temperature from 50C to 80C
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Chen, M.; Narai, S.; Omura, N.; Shigi, N.; Chimnaronk, S.; Tanaka, Y.; Yao, M.
Identification Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA-TtuB from Thermus thermophilus
Acta Crystallogr. Sect. F
72
777.781
2016
Thermus thermophilus (Q72LF3), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
Shigi, N.; Sakaguchi, Y.; Suzuki, T.; Watanabe, K.
Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures
J. Biol. Chem.
281
14296-306
2006
Thermus thermophilus (Q72LF3), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
Shigi, N.; Suzuki, T.; Terade, T.; Shirouzu, M.; Yokoyama, S.; Watanabe, K.
Identification Temperature-dependent biosynthesis of 2-thioribothymidine of Thermus thermophilus tRNA
J. Biol. Chem.
281
2104-2113
2006
Thermus thermophilus (Q72LF3), Thermus thermophilus DSM 7039 (Q72LF3), Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q72LF3)
brenda
Nakagawa, H.; Kuratani, M.; Goto-Ito, S.; Ito, T.; Katsura, K.; Terada, T.; Shirouzu, M.; Sekine, S.; Shigi, N.; Yokoyama, S.
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA
Proteins
81
1232-1244
2013
Pyrococcus horikoshii (O58038), Thermus thermophilus (Q72LF3), Pyrococcus horikoshii DSM 12428 (O58038), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
Chen, M.; Narai, S.; Omura, N.; Shigi, N.; Chimnaronk, S.; Tanaka, Y.; Yao, M.
Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA-TtuB from Thermus thermophilus
Acta Crystallogr. Sect. F
72
777-781
2016
Thermus thermophilus (Q72LF3), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
Shigi, N.; Asai, S.; Watanabe, K.
Identification of a rhodanese-like protein involved in thiouridine biosynthesis in Thermus thermophilus tRNA
FEBS Lett.
590
4628-4637
2016
Thermus thermophilus (Q72LF3), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
Shigi, N.; Sakaguchi, Y.; Suzuki, T.; Watanabe, K.
Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures
J. Biol. Chem.
281
14296-14306
2006
Thermus thermophilus (Q72LF3), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
Chen, M.; Asai, S.; Narai, S.; Nambu, S.; Omura, N.; Sakaguchi, Y.; Suzuki, T.; Ikeda-Saito, M.; Watanabe, K.; Yao, M.; Shigi, N.; Tanaka, Y.
Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA
Proc. Natl. Acad. Sci. USA
114
4954-4959
2017
Thermus thermophilus (Q72LF3), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
Nakagawa, H.; Kuratani, M.; Goto-Ito, S.; Ito, T.; Katsura, K.; Terada, T.; Shirouzu, M.; Sekine, S.; Shigi, N.; Yokoyama, S.
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA
Proteins Struct. Funct. Bioinform.
81
1232-1244
2013
Pyrococcus horikoshii (O58038), Thermus thermophilus (Q72LF3), Pyrococcus horikoshii DSM 12428 (O58038), Thermus thermophilus DSM 7039 (Q72LF3)
brenda
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Release 2023.1 (January 2023)
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