title: Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma.
abstract: Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly. One checkpoint is the AlaRS editing centre, and the other is from widely distributed AlaXps-free-standing, genome-encoded editing proteins that clear Ser-tRNA(Ala). The paradox of misincorporating both a smaller (glycine) and a larger (serine) amino acid suggests a deep conflict for nature-designed AlaRS. Here we show the chemical basis for this conflict. Nine crystal structures, together with kinetic and mutational analysis, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the alpha-amino group of the bound amino acid by using an acidic residue. This design, dating back more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently because no better architecture for the recognition of alanine could be found, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.
authors.affiliation: The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Guo
authors.forename: Yeeting E
authors.initials: YE
authors.lastname: Chong
authors.forename: Ryan
authors.initials: R
authors.lastname: Shapiro
authors.forename: Kirk
authors.initials: K
authors.lastname: Beebe
authors.forename: Xiang-Lei
authors.initials: XL
authors.lastname: Yang
authors.forename: Paul
authors.initials: P
authors.lastname: Schimmel
mesh_terms: D000409:Alanine / Q000378:metabolism*; D000412:Alanine-tRNA Ligase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001224:Aspartic Acid / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D003460:Crystallization; D004926:Escherichia coli / Q000201:enzymology*; D007700:Kinetics; D008958:Models, Molecular; D009154:Mutation; D014176:Protein Biosynthesis; D011487:Protein Conformation; D012344:RNA, Transfer, Ala / Q000378:metabolism; D012694:Serine / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D012344:RNA, Transfer, Ala; D001224:Aspartic Acid; D012694:Serine; D000412:Alanine-tRNA Ligase; D000409:Alanine