Rhea - reaction knowledgebase

Enzymes

UniProtKB ^help_outline	1,866 proteins
Enzyme class ^help_outline	EC 6.3.4.22 tRNA(Ile)(2)-agmatinylcytidine synthase

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Name ^help_outline agmatine Identifier CHEBI:58145 Charge 2 Formula C5H16N4 InChIKey^help_outline QYPPJABKJHAVHS-UHFFFAOYSA-P SMILES^help_outline NC(=[NH2+])NCCCC[NH3+] 2D coordinates Mol file for the small molecule Search links Involved in 15 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline ATP Identifier CHEBI:30616 (Beilstein: 3581767) ^help_outline Charge -4 Formula C10H12N5O13P3 InChIKey^help_outline ZKHQWZAMYRWXGA-KQYNXXCUSA-J SMILES^help_outline Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)[C@@H](O)[C@H]1O 2D coordinates Mol file for the small molecule Search links Involved in 1,280 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name^help_outline cytidine³⁴ in tRNA^Ile2 Identifier RHEA-COMP:10625 Reactive part ^help_outline
- Name ^help_outline CMP residue Identifier CHEBI:82748 Charge -1 Formula C9H11N3O7P Position^help_outline 34 SMILES^help_outline Nc1ccn([C@@H]2O[C@H](COP([O-])(-*)=O)[C@@H](O-*)[C@H]2O)c(=O)n1 2D coordinates Mol file for the small molecule Search links Involved in 66 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Search links Involved in 2 reaction(s) Find proteins in UniProtKB for this molecule
Name ^help_outline H₂O Identifier CHEBI:15377 (Beilstein: 3587155; CAS: 7732-18-5) ^help_outline Charge 0 Formula H2O InChIKey^help_outline XLYOFNOQVPJJNP-UHFFFAOYSA-N SMILES^help_outline [H]O[H] 2D coordinates Mol file for the small molecule Search links Involved in 6,204 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name^help_outline 2-agmatinylcytidine³⁴ in tRNA^Ile2 Identifier RHEA-COMP:10626 Reactive part ^help_outline
- Name ^help_outline agmatidine 5'-phosphate residue Identifier CHEBI:83545 Charge 1 Formula C14H25N7O6P Position^help_outline 34 SMILES^help_outline NC(=[NH2+])NCCCCNc1[nH+]c(=N)ccn1[C@@H]1O[C@H](COP([O-])(-*)=O)[C@@H](O-*)[C@H]1O 2D coordinates Mol file for the small molecule Search links Involved in 1 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Search links Involved in 1 reaction(s) Find proteins in UniProtKB for this molecule
Name ^help_outline AMP Identifier CHEBI:456215 Charge -2 Formula C10H12N5O7P InChIKey^help_outline UDMBCSSLTHHNCD-KQYNXXCUSA-L SMILES^help_outline Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP([O-])([O-])=O)[C@@H](O)[C@H]1O 2D coordinates Mol file for the small molecule Search links Involved in 508 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline H⁺ Identifier CHEBI:15378 Charge 1 Formula H InChIKey^help_outline GPRLSGONYQIRFK-UHFFFAOYSA-N SMILES^help_outline [H+] 2D coordinates Mol file for the small molecule Search links Involved in 9,431 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline phosphate Identifier CHEBI:43474 Charge -2 Formula HO4P InChIKey^help_outline NBIIXXVUZAFLBC-UHFFFAOYSA-L SMILES^help_outline OP([O-])([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 992 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule

Cross-references

	RHEA:43608	RHEA:43609	RHEA:43610	RHEA:43611
Reaction direction	undefined	left-to-right	right-to-left	bidirectional
UniProtKB ^help_outline	1,866 proteins
EC numbers ^help_outline	6.3.4.22
KEGG ^help_outline				R10496
MetaCyc ^help_outline		RXN-14344

Publications

Crystallization and preliminary X-ray diffraction analysis of an archaeal tRNA-modification enzyme, TiaS, complexed with tRNA(Ile2) and ATP.

Osawa T., Inanaga H., Kimura S., Terasaka N., Suzuki T., Numata T.

The cytidine at the first anticodon position of archaeal tRNA(Ile2), which decodes the isoleucine AUA codon, is modified to 2-agmatinylcytidine (agm(2)C) to guarantee the fidelity of protein biosynthesis. This post-transcriptional modification is catalyzed by tRNA(Ile)-agm(2)C synthetase (TiaS) us ... >> More

The cytidine at the first anticodon position of archaeal tRNA(Ile2), which decodes the isoleucine AUA codon, is modified to 2-agmatinylcytidine (agm(2)C) to guarantee the fidelity of protein biosynthesis. This post-transcriptional modification is catalyzed by tRNA(Ile)-agm(2)C synthetase (TiaS) using ATP and agmatine as substrates. Archaeoglobus fulgidus TiaS was overexpressed in Escherichia coli cells and purified. tRNA(Ile2) was prepared by in vitro transcription with T7 RNA polymerase. TiaS was cocrystallized with both tRNA(Ile2) and ATP by the vapour-diffusion method. The crystals of the TiaS-tRNA(Ile2)-ATP complex diffracted to 2.9 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the primitive hexagonal space group P3(2)21, with unit-cell parameters a = b = 131.1, c = 86.6 Å. The asymmetric unit is expected to contain one TiaS-tRNA(Ile2)-ATP complex, with a Matthews coefficient of 2.8 Å(3) Da(-1) and a solvent content of 61%. << Less

Acta Crystallogr Sect F Struct Biol Cryst Commun 67:1414-1416(2011) [PubMed] [EuropePMC]
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea.

Ikeuchi Y., Kimura S., Numata T., Nakamura D., Yokogawa T., Ogata T., Wada T., Suzuki T., Suzuki T.

A modified base at the first (wobble) position of some tRNA anticodons is critical for deciphering the genetic code. In eukaryotes and eubacteria, AUA codons are decoded by tRNAsIle with modified bases pseudouridine (and/or inosine) and lysidine, respectively. The mechanism by which archaeal speci ... >> More

A modified base at the first (wobble) position of some tRNA anticodons is critical for deciphering the genetic code. In eukaryotes and eubacteria, AUA codons are decoded by tRNAsIle with modified bases pseudouridine (and/or inosine) and lysidine, respectively. The mechanism by which archaeal species translate AUA codons is unclear. We describe a polyamine-conjugated modified base, 2-agmatinylcytidine (agm(2)C or agmatidine), at the wobble position of archaeal tRNA(Ile) that decodes AUA codons specifically. We demonstrate that archaeal cells use agmatine to synthesize agm(2)C of tRNA(Ile). We also identified a new enzyme, tRNA(Ile)-agm(2)C synthetase (TiaS), that catalyzes agm(2)C formation in the presence of agmatine and ATP. Although agm(2)C is chemically similar to lysidine, TiaS constitutes a distinct class of enzyme from tRNA(Ile)-lysidine synthetase (TilS), suggesting that the decoding systems evolved convergently across domains. << Less

Nat. Chem. Biol. 6:277-282(2010) [PubMed] [EuropePMC]
Tricuspid valve infective endocarditis and pulmonary sepsis due to Erysipelothrix rhusiopathiae successfully treated with high doses of ciprofloxacin but complicated by gynaecomastia.

MacGowan A.P., Reeves D.S., Wright C., Glover S.C.

J Infect 22:100-101(1991) [PubMed] [EuropePMC]

RHEA:43608 agmatine + ATP + cytidine(34) in tRNA(Ile2) + H2O = 2-agmatinylcytidine(34) in tRNA(Ile2) + AMP + 2 H(+) + 2 phosphate

Enzymes

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Cross-references

Publications

Crystallization and preliminary X-ray diffraction analysis of an archaeal tRNA-modification enzyme, TiaS, complexed with tRNA(Ile2) and ATP.

Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea.

Tricuspid valve infective endocarditis and pulmonary sepsis due to Erysipelothrix rhusiopathiae successfully treated with high doses of ciprofloxacin but complicated by gynaecomastia.