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Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition

Academic Article
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Overview

related to degree

  • Lovato-Tse, Martha, Ph.D. in Chemistry, Scripps Research 1998 - 2003

authors

  • Swairjo, M. A.
  • Otero, F. J.
  • Yang, Xiang-Lei
  • Lovato-Tse, Martha
  • Skene, R. J.
  • McRee, Duncan
  • Ribas de Pouplana, L.
  • Schimmel, Paul

publication date

  • March 2004

journal

  • Molecular Cell  Journal

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.

subject areas

  • Alanine-tRNA Ligase
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Bacterial Proteins
  • Base Pairing
  • Binding Sites
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Escherichia coli
  • Hydrophobic and Hydrophilic Interactions
  • Kinetics
  • Models, Molecular
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA, Bacterial
  • Sequence Homology, Amino Acid
  • Substrate Specificity
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Identity

International Standard Serial Number (ISSN)

  • 1097-2765

Digital Object Identifier (DOI)

  • 10.1016/s1097-2765(04)00126-1

PubMed ID

  • 15053876
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Additional Document Info

start page

  • 829

end page

  • 841

volume

  • 13

issue

  • 6

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