title: Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition.
abstract: Early work on aminoacylation of alanine-specific tRNA (tRNA(Ala)) by alanyl-tRNA synthetase (AlaRS) gave rise to the concept of an early "second genetic code" imbedded in the acceptor stems of tRNAs. A single conserved and position-specific G:U base pair in the tRNA acceptor stem is the key identity determinant. Further understanding has been limited due to lack of a crystal structure of the enzyme. We determined a 2.14 A crystal structure of the 453 amino acid catalytic fragment of Aquifex aeolicus AlaRS. It contains the catalytic domain characteristic of class II synthetases, a helical domain with a hairpin motif critical for acceptor-stem recognition, and a C-terminal domain of a mixed alpha/beta fold. Docking of tRNA(Ala) on AlaRS shows critical contacts with the three domains, consistent with previous mutagenesis and functional data. It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA(Ala)s.
authors.affiliation: Skaags Institute for Chemical Biology, Departments of Molecular Biology and Chemistry, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Manal A
authors.initials: MA
authors.lastname: Swairjo
authors.forename: Francella J
authors.initials: FJ
authors.lastname: Otero
authors.forename: Xiang-Lei
authors.initials: XL
authors.lastname: Yang
authors.forename: Martha A
authors.initials: MA
authors.lastname: Lovato
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Skene
authors.forename: Duncan E
authors.initials: DE
authors.lastname: McRee
authors.forename: Lluis
authors.initials: L
authors.lastname: Ribas de Pouplana
authors.forename: Paul
authors.initials: P
authors.lastname: Schimmel
mesh_terms: D000412:Alanine-tRNA Ligase / Q000737:chemistry* / Q000235:genetics; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D020029:Base Pairing; D001665:Binding Sites; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D000412:Alanine-tRNA Ligase