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Literature summary for 2.6.1.B20 extracted from

  • Yokogawa, T.; Nomura, Y.; Yasuda, A.; Ogino, H.; Hiura, K.; Nakada, S.; Oka, N.; Ando, K.; Kawamura, T.; Hirata, A.; Hori, H.; Ohno, S.
    Identification of a radical SAM enzyme involved in the synthesis of archaeosine (2019), Nat. Chem. Biol., 15, 1148-1155 .
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
recombinant coexpression of His-tagged TaArcS and His-tagged TkRaSEA in Escherichia coli Thermococcus kodakarensis
recombinant coexpression of His-tagged wild-type and mutant enzymes in Escherichia coli strain ER2566 Methanosarcina acetivorans

Protein Variants

Protein Variants Comment Organism
C51A site-directed mutagenesis of a residue from the radical SAM enzymes' conserved CX3CX2C motif. No T1 fragment containing G+ is detected, but signals of U(s4U)AACAAA(q0kN)CGp are observed in the T1 fragments of tRNACys from C51A-expressing cells Methanosarcina acetivorans
C59A site-directed mutagenesis of a residue from the radical SAM enzymes' conserved CX3CX2C motif. No T1 fragment containing G+ is detected, but signals of U(s4U)AACAAA(q0kN)CGp are observed in the T1 fragments of tRNACys from C59A-expressing cells Methanosarcina acetivorans
C62A site-directed mutagenesis of a residue from the radical SAM enzymes' conserved CX3CX2C motif. No T1 fragment containing G+ is detected, but signals of U(s4U)AACAAA(q0kN)CGp are observed in the T1 fragments of tRNACys from C62A-expressing cells Methanosarcina acetivorans
additional information construction of a TK1135 disruption strain (DELTATK1135). The G+ peak disappears from the tRNA fraction of strain DELTATK1135 and a small q0kN peak is observed Thermococcus kodakarensis

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ in the [4Fe-4S] cluster Methanosarcina acetivorans

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine Thermococcus kodakarensis reaction of subunit beta 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine Methanosarcina acetivorans reaction of subunit beta 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine Methanosarcina acetivorans ATCC 35395 reaction of subunit beta 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine Thermococcus kodakarensis JCM 12380 reaction of subunit beta 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine Methanosarcina acetivorans DSM 2834 reaction of subunit beta 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine Methanosarcina acetivorans JCM 12185 reaction of subunit beta 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine Thermococcus kodakarensis ATCC BAA-918 reaction of subunit beta 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?

Organism

Organism UniProt Comment Textmining
Methanosarcina acetivorans Q8THK1 ArcS subunit beta
-
Methanosarcina acetivorans ATCC 35395 Q8THK1 ArcS subunit beta
-
Methanosarcina acetivorans DSM 2834 Q8THK1 ArcS subunit beta
-
Methanosarcina acetivorans JCM 12185 Q8THK1 ArcS subunit beta
-
Thermococcus kodakarensis Q5JE80 ArcS subunit beta
-
Thermococcus kodakarensis ATCC BAA-918 Q5JE80 ArcS subunit beta
-
Thermococcus kodakarensis JCM 12380 Q5JE80 ArcS subunit beta
-

Purification (Commentary)

Purification (Comment) Organism
copurification of recombinant His-tagged TaArcS and His-tagged TkRaSEA from Escherichia coli by nickel affinity chromatography Thermococcus kodakarensis
copurification of recombinant His-tagged wild-type and mutant enzyme complexes from Escherichia coli by nickel affinity chromatography Methanosarcina acetivorans

Reaction

Reaction Comment Organism Reaction ID
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine = 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine reaction mechanism of RaSEA, overview Thermococcus kodakarensis
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine = 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine reaction mechanism of RaSEA, overview Methanosarcina acetivorans

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta Thermococcus kodakarensis 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta Methanosarcina acetivorans 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta. G+ is successfully synthesized in recombinant Escherichia coli cells by MaArcTGT and the MaArcS-MaRaSEA complex Methanosarcina acetivorans 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta Methanosarcina acetivorans ATCC 35395 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta. G+ is successfully synthesized in recombinant Escherichia coli cells by MaArcTGT and the MaArcS-MaRaSEA complex Methanosarcina acetivorans ATCC 35395 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta Thermococcus kodakarensis JCM 12380 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta Methanosarcina acetivorans DSM 2834 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta. G+ is successfully synthesized in recombinant Escherichia coli cells by MaArcTGT and the MaArcS-MaRaSEA complex Methanosarcina acetivorans DSM 2834 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta Methanosarcina acetivorans JCM 12185 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta. G+ is successfully synthesized in recombinant Escherichia coli cells by MaArcTGT and the MaArcS-MaRaSEA complex Methanosarcina acetivorans JCM 12185 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?
7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-deazaguanosine15 in tRNA + S-adenosyl-L-methionine reaction of subunit beta Thermococcus kodakarensis ATCC BAA-918 5'-deoxyadenosine + archaeosine15 in tRNA + 2 H+ + L-1-piperideine-6-carboxylate + L-methionine
-
?

Synonyms

Synonyms Comment Organism
archaeosine synthase subunit beta
-
Thermococcus kodakarensis
archaeosine synthase subunit beta
-
Methanosarcina acetivorans
MaRaSEA
-
Methanosarcina acetivorans
MA_4513
-
Methanosarcina acetivorans
q0kN-tRNA lyase
-
Thermococcus kodakarensis
q0kN-tRNA lyase
-
Methanosarcina acetivorans
RaSEA
-
Thermococcus kodakarensis
RaSEA
-
Methanosarcina acetivorans
TK1135 locus name of subunit beta Thermococcus kodakarensis
TkRaSEA
-
Thermococcus kodakarensis

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine subunit B is a SAM radical enzyme Thermococcus kodakarensis
S-adenosyl-L-methionine subunit B is a SAM radical enzyme Methanosarcina acetivorans
[4Fe-4S] cluster
-
Methanosarcina acetivorans

General Information

General Information Comment Organism
evolution the hyperthermophilic euryarchaeon Thermococcus kodakarensis lacks an arcTGT orthologue Thermococcus kodakarensis
evolution the hyperthermophilic euryarchaeon Thermococcus kodakarensis lacks an arcTGT orthologue Methanosarcina acetivorans
malfunction in a TK1135 disruption strain (DELTATK1135), the G+ peak disappears from the tRNA fraction and a small q0kN peak is observed Thermococcus kodakarensis
malfunction in a TK1135 disruption strain (DELTATK1135), the G+ peak disappears from the tRNA fraction and a small q0kN peak is observed Methanosarcina acetivorans
metabolism archaeosine biosynthesis pathway, overview Thermococcus kodakarensis
metabolism archaeosine biosynthesis pathway, overview Methanosarcina acetivorans
additional information the archaeosine synthases from Thermococcus kodakarensis is composed of ArcS (subunit alpha) and the radical SAM enzyme TkRaSEA (q0kN-tRNA lyase, subunit beta) both forming a robust complex, but the interaction between TkRaSEA and Thermoplasma acidophilum ArcS is considerably weaker. Interaction analysis, overview Thermococcus kodakarensis
additional information the archaeosine synthases from Thermococcus kodakarensis is composed of ArcS (subunit alpha) and the radical SAM enzyme TkRaSEA (q0kN-tRNA lyase, subunit beta) both forming a robust complex, but the interaction between TkRaSEA and Thermoplasma acidophilum ArcS is considerably weaker. Interaction analysis, overview. Residues C51, C59 and C62 in the conserved CX3CX2C motif of radical SAM enzyme MaRaSEA are involved in G+ formation and coordinate iron atoms of the [4Fe-4S] cluster in MaRaSEA Methanosarcina acetivorans
physiological function archaeosine (G+), 7-formamidino-7-deazaguanosine, is an archaea-specific modified nucleoside found at the 15th position of tRNAs. In Euryarchaeota, 7-cyano-7-deazaguanine (preQ0)-containing tRNA (q0N-tRNA), synthesized by archaeal tRNA-guanine transglycosylase (ArcTGT), is converted to G+-containing tRNA (G+-tRNA) by the paralogue of ArcTGT, ArcS. Several euryarchaeal ArcSs have lysine transfer activity to q0N-tRNA to form q0kN-tRNA, which has a preQ0 lysine adduct as a base. ArcS forms a robust complex with a radical S-adenosylmethionine (SAM) enzyme named RaSEA. The ArcS-RaSEA complex anaerobically converts q0N-tRNA to G+-tRNA in the presence of SAM and lysine via q0kN-tRNA. It is proposed that ArcS and RaSEA should be considered an archaeosine synthase alpha-subunit (lysine transferase) and beta-subunit (q0kN-tRNA lyase), respectively. The TK1135 product is involved in G+ biosynthesis and q0kN is an intermediate in the synthesis of G+ Thermococcus kodakarensis
physiological function archaeosine (G+), 7-formamidino-7-deazaguanosine, is an archaea-specific modified nucleoside found at the 15th position of tRNAs. In Euryarchaeota, 7-cyano-7-deazaguanine (preQ0)-containing tRNA (q0N-tRNA), synthesized by archaeal tRNA-guanine transglycosylase (ArcTGT), is converted to G+-containing tRNA (G+-tRNA) by the paralogue of ArcTGT, ArcS. Several euryarchaeal ArcSs have lysine transfer activity to q0N-tRNA to form q0kN-tRNA, which has a preQ0 lysine adduct as a base. ArcS forms a robust complex with a radical S-adenosylmethionine (SAM) enzyme named RaSEA. The ArcS-RaSEA complex anaerobically converts q0N-tRNA to G+-tRNA in the presence of SAM and lysine via q0kN-tRNA. It is proposed that ArcS and RaSEA should be considered an archaeosine synthase alpha-subunit (lysine transferase) and beta-subunit (q0kN-tRNA lyase), respectively. The TK1135 product is involved in G+ biosynthesis and q0kN is an intermediate in the synthesis of G+ Methanosarcina acetivorans