title: Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.
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.
authors.affiliation: Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA. jungwook.kim@einstein.yu.edu
authors.forename: Jungwook
authors.initials: J
authors.lastname: Kim
authors.forename: Hui
authors.initials: H
authors.lastname: Xiao
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Bonanno
authors.forename: Chakrapani
authors.initials: C
authors.lastname: Kalyanaraman
authors.forename: Shoshana
authors.initials: S
authors.lastname: Brown
authors.forename: Xiangying
authors.initials: X
authors.lastname: Tang
authors.forename: Nawar F
authors.initials: NF
authors.lastname: Al-Obaidi
authors.forename: Yury
authors.initials: Y
authors.lastname: Patskovsky
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Babbitt
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Jacobson
authors.forename: Young-Sam
authors.initials: YS
authors.lastname: Lee
authors.forename: Steven C
authors.initials: SC
authors.lastname: Almo
mesh_terms: D055162:Biocatalysis; D053898:Biosynthetic Pathways; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003509:Cyclohexanecarboxylic Acids / Q000378:metabolism; D053138:Cyclohexenes / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008024:Ligands; D008780:Methyltransferases / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008970:Molecular Weight; D019875:One-Carbon Group Transferases / Q000737:chemistry / Q000378:metabolism*; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012436:S-Adenosylmethionine / Q000031:analogs & derivatives* / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism*; D014529:Uridine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism
chemical_list: C581857:4-(((5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(carboxylatomethyl)sulfonio)-2-ammoniobutanoate; D003509:Cyclohexanecarboxylic Acids; D053138:Cyclohexenes; D029968:Escherichia coli Proteins; D008024:Ligands; D012329:RNA, Bacterial; C025230:uridine-5-oxyacetic acid; D012436:S-Adenosylmethionine; D012343:RNA, Transfer; C010194:5-hydroxyuridine; C581858:CmoA protein, E coli; D019875:One-Carbon Group Transferases; C581859:CmoB protein, E coli; D008780:Methyltransferases; D014529:Uridine; C005550:prephenic acid