title: Molecular basis of alanine discrimination in editing site.
abstract: AlaX is the homologue of the class II alanyl-tRNA synthetase editing domain and has been shown to exhibit autonomous editing activity against mischarged tRNA(Ala). Here, we present the structures of AlaX from the archaeon Pyrococcus horikoshii in apo form, complexed with zinc, and with noncognate amino acid l-serine and zinc. Together with mutational analysis, we demonstrated that the conserved Thr-30 hydroxyl group located near the beta-methylene of the bound serine is responsible for the discrimination of noncognate serine from cognate alanine, based on their chemical natures. Furthermore, we confirmed that the conserved Gln-584 in alanyl-tRNA synthetase, which corresponds to Thr-30 of AlaX, is also critical for discrimination. These observations strongly suggested conservation of the chemical discrimination among trans- and cis-editing of tRNA(Ala).
authors.affiliation: Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Sokabe
authors.forename: Ayuko
authors.initials: A
authors.lastname: Okada
authors.forename: Min
authors.initials: M
authors.lastname: Yao
authors.forename: Takashi
authors.initials: T
authors.lastname: Nakashima
authors.forename: Isao
authors.initials: I
authors.lastname: Tanaka
mesh_terms: D000215:Acylation; D000409:Alanine / Q000235:genetics* / Q000378:metabolism*; D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001051:Apoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D019281:Dimerization; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D043902:Pyrococcus horikoshii / Q000201:enzymology; D017393:RNA Editing; D012344:RNA, Transfer, Ala / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D012694:Serine / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D013912:Threonine / Q000235:genetics / Q000378:metabolism; D015032:Zinc / Q000378:metabolism
chemical_list: D001051:Apoenzymes; D001426:Bacterial Proteins; D012344:RNA, Transfer, Ala; D013912:Threonine; D012694:Serine; D000604:Amino Acyl-tRNA Synthetases; D015032:Zinc; D000409:Alanine