4GEK

Crystal Structure of wild-type CmoA from E.coli

Summary for 4GEK

• Entry DOI: 10.2210/pdb4gek/pdb
• Descriptor: tRNA (cmo5U34)-methyltransferase, SULFATE ION, (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate, ... (4 entities in total)
• Functional Keywords: structural genomics, psi-biology, new york structural genomics research consortium, nysgrc, rossmann fold, synthase, sam prephenate, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 60262.16

Authors

Kim, J.,Toro, R.,Bonanno, J.B.,Bhosle, R.,Sampathkumar, P.,Almo, S.C.,New York Structural Genomics Research Consortium (NYSGRC) (deposition date: 2012-08-02, release date: 2012-10-10, Last modification date: 2023-09-13)

Primary citation

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.
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function
Nature, 498:123-126, 2013

PubMed Abstract: 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.

PubMed: 23676670
DOI: 10.1038/nature12180

Experimental method

X-RAY DIFFRACTION (1.5 Å)