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Protein-Nucleic Acid Interaction: A Modified SAM to Modify tRNA

SBKB [doi:10.1038/sbkb.2012.149]
Featured Article - July 2013
Short description: Basic metabolism may seem quite old-school, but the structure of a biosynthetic enzyme offers several surprises.

Stick representation of the computationally predicted pose of prephenate (grey) in the CmoA catalytic site. Protein carbon atoms are shown in green; oxygen and nitrogen atoms are shown in red and blue, respectively. Ionic interactions between prephenate and CmoA side chains are depicted as dashed lines (distances in Å). 1

Transfer RNAs, which bind and escort amino acids to the ribosome, are remarkable for their variety of modifications, particularly at the 5′ nucleotide of the anticodon sequence. One such modification is 5-oxyacetyl uridine (cmo5U). The formation of cmo5U from hydroxyl uridine (ho5U) in bacteria was known to involve enzymes CmoA and CmoB and to use S-adenosyl-L-methionine (SAM), but the precise mechanism remained to be determined.

In solving the structure of Escherichia coli CmoA (PDB 4GEK), Kim, Almo and colleagues (PSI NYSGRC) discovered a novel metabolite, carboxy-SAM (Cx-SAM), in its hydrophobic catalytic site. Residues interacting with Cx-SAM are conserved among bacterial CmoA orthologs, but not in other members of this class of SAM-dependent methyltransferases. In vitro analysis of Cx-SAM formation revealed yet another unexpected facet of the reaction: prephenate was used more efficiently by CmoA as the carboxyl donor, rather than the expected chorismate. When a prephenate molecule was docked into the structure, there was another surprise: whereas other SAM-dependent methyltransfer reactions use a linear SN2-based reaction, it appeared, and was subsequently confirmed in vitro, that CmoA used a mechanism involving an unusual reactive sulphonium ylide (stabilized carbanion) intermediate.

The remaining question was the role of CmoB. By co-incubating prephenate, SAM, CmoA, CmoB and ho5U-containing RNA, the authors demonstrated that CmoB, but not CmoA, mediates carboxymethyl transfer from Cx-SAM to ho5U-modified RNA, resulting in RNA containing the cmo5U modification.

The S-methyl group of SAM has been a favored target of chemists seeking modification of both proteins and nucleic acids. Cx-SAM is the first example of a physiologically relevant modified SAM, and its identification will certainly drive the search for other SAM derivatives. In addition, this work highlights the power of structural biology to identify unanticipated ligands that may alter enzymatic activity.

Angela K. Eggleston

References

  1. J. Kim et al. Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.
    Nature 498, 123-126 (2013). doi:10.1038/nature12180

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