Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

PLoS Comput Biol. 2018 Apr 16;14(4):e1006101. doi: 10.1371/journal.pcbi.1006101. eCollection 2018 Apr.

Abstract

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Amino Acyl-tRNA Synthetases / classification*
  • Amino Acyl-tRNA Synthetases / genetics
  • Amino Acyl-tRNA Synthetases / metabolism*
  • Arginine / chemistry
  • Base Sequence
  • Catalytic Domain / genetics
  • Codon / genetics
  • Computational Biology
  • Evolution, Molecular
  • Genetic Variation
  • Humans
  • Ligands
  • Models, Molecular
  • Mutagenesis
  • Protein Conformation
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism

Substances

  • Codon
  • Ligands
  • Adenosine Triphosphate
  • RNA, Transfer
  • Arginine
  • Amino Acyl-tRNA Synthetases

Grants and funding

This work was funded by the European Social Fund (http://ec.europa.eu/esf/, grant numbers: 100235472 for FK and 1463643413126 for CL), the Free State of Saxony and the Saxon Ministry of Fine Arts. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.