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

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

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.

Details

Original languageEnglish
Article numbere1006101
JournalPLOS computational biology
Volume14
Issue number4
Publication statusPublished - Apr 2018
Peer-reviewedYes

External IDs

PubMedCentral PMC5919687
Scopus 85046345979
ORCID /0000-0003-2848-6949/work/141543369

Keywords

Keywords

  • Adenosine Triphosphate/metabolism, Amino Acid Sequence, Amino Acyl-tRNA Synthetases/classification, 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

Library keywords