Enzymes
UniProtKB help_outline | 4,666 proteins |
Reaction participants Show >> << Hide
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Namehelp_outline
5-hydroxyuridine34 in tRNA
Identifier
RHEA-COMP:13381
Reactive part
help_outline
- Name help_outline 5-(hydroxy)uridine 5'-phosphate residue Identifier CHEBI:136877 Charge -1 Formula C9H10N2O9P Positionhelp_outline 34 SMILEShelp_outline C1=C(C(NC(N1[C@@H]2O[C@H](COP(*)(=O)[O-])[C@H]([C@H]2O)O*)=O)=O)O 2D coordinates Mol file for the small molecule Search links Involved in 3 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline carboxy-S-adenosyl-L-methionine Identifier CHEBI:134278 Charge 0 Formula C16H22N6O7S InChIKeyhelp_outline VFFTYSZNZJBRBG-DYXDMYNLSA-N SMILEShelp_outline C([S+](CC[C@H]([NH3+])C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=NC3=C2N=CN=C3N)C([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
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Namehelp_outline
5-carboxymethoxyuridine34 in tRNA
Identifier
RHEA-COMP:13383
Reactive part
help_outline
- Name help_outline 5-(carboxymethoxy)uridine 5'-phosphate residue Identifier CHEBI:136879 Charge -2 Formula C11H11N2O11P Positionhelp_outline 34 SMILEShelp_outline C1=C(C(NC(N1[C@@H]2O[C@H](COP(*)(=O)[O-])[C@H]([C@H]2O)O*)=O)=O)OCC([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 2 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 InChIKeyhelp_outline GPRLSGONYQIRFK-UHFFFAOYSA-N SMILEShelp_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 S-adenosyl-L-homocysteine Identifier CHEBI:57856 Charge 0 Formula C14H20N6O5S InChIKeyhelp_outline ZJUKTBDSGOFHSH-WFMPWKQPSA-N SMILEShelp_outline Nc1ncnc2n(cnc12)[C@@H]1O[C@H](CSCC[C@H]([NH3+])C([O-])=O)[C@@H](O)[C@H]1O 2D coordinates Mol file for the small molecule Search links Involved in 792 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Cross-references
RHEA:52848 | RHEA:52849 | RHEA:52850 | RHEA:52851 | |
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Reaction direction help_outline | undefined | left-to-right | right-to-left | bidirectional |
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Publications
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Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.
Kim J., Xiao H., Koh J., Wang Y., Bonanno J.B., Thomas K., Babbitt P.C., Brown S., Lee Y.S., Almo S.C.
Enzyme-mediated modifications at the wobble position of tRNAs are essential for the translation of the genetic code. We report the genetic, biochemical and structural characterization of CmoB, the enzyme that recognizes the unique metabolite carboxy-S-adenosine-L-methionine (Cx-SAM) and catalyzes ... >> More
Enzyme-mediated modifications at the wobble position of tRNAs are essential for the translation of the genetic code. We report the genetic, biochemical and structural characterization of CmoB, the enzyme that recognizes the unique metabolite carboxy-S-adenosine-L-methionine (Cx-SAM) and catalyzes a carboxymethyl transfer reaction resulting in formation of 5-oxyacetyluridine at the wobble position of tRNAs. CmoB is distinctive in that it is the only known member of the SAM-dependent methyltransferase (SDMT) superfamily that utilizes a naturally occurring SAM analog as the alkyl donor to fulfill a biologically meaningful function. Biochemical and genetic studies define the in vitro and in vivo selectivity for Cx-SAM as alkyl donor over the vastly more abundant SAM. Complementary high-resolution structures of the apo- and Cx-SAM bound CmoB reveal the determinants responsible for this remarkable discrimination. Together, these studies provide mechanistic insight into the enzymatic and non-enzymatic feature of this alkyl transfer reaction which affords the broadened specificity required for tRNAs to recognize multiple synonymous codons. << Less
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Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.
Kim J., Xiao H., Bonanno J.B., Kalyanaraman C., Brown S., Tang X., Al-Obaidi N.F., Patskovsky Y., Babbitt P.C., Jacobson M.P., Lee Y.S., Almo S.C.
The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights ... >> More
The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights into new activities, pathways and regulatory mechanisms. We describe a new metabolite, carboxy-S-adenosyl-l-methionine (Cx-SAM), its biosynthetic pathway and its role in transfer RNA modification. The structure of CmoA, a member of the SAM-dependent methyltransferase superfamily, revealed a ligand consistent with Cx-SAM in the catalytic site. Mechanistic analyses showed an unprecedented role for prephenate as the carboxyl donor and the involvement of a unique ylide intermediate as the carboxyl acceptor in the CmoA-mediated conversion of SAM to Cx-SAM. A second member of the SAM-dependent methyltransferase superfamily, CmoB, recognizes Cx-SAM and acts as a carboxymethyltransferase to convert 5-hydroxyuridine into 5-oxyacetyl uridine at the wobble position of multiple tRNAs in Gram-negative bacteria, resulting in expanded codon-recognition properties. CmoA and CmoB represent the first documented synthase and transferase for Cx-SAM. These findings reveal new functional diversity in the SAM-dependent methyltransferase superfamily and expand the metabolic and biological contributions of SAM-based biochemistry. These discoveries highlight the value of structural genomics approaches in identifying ligands within the context of their physiologically relevant macromolecular binding partners, and in revealing their functions. << Less
Nature 498:123-126(2013) [PubMed] [EuropePMC]
This publication is cited by 1 other entry.