Transfer RNAs (tRNAs) are RNA molecules used by all forms of life, from bacteria to plants to humans, to transfer amino acids to growing protein molecules that have been coded by DNA and transcribed into messenger RNA (mRNA) for translation by ribosomes into proteins. This is one of the most basic, crucial processes of life.
However, tRNAs do more than just perform this essential function and are known to have regulatory roles in translation, transcription, stress response, and even immunity, via specific interactions with a wide array of cellular molecules. Disruption of these interactions has also been shown to be associated with some types of neurological disease and cancer, making it critical to understand how proteins in the cell recognize tRNAs.
Many different proteins have been shown to interact with tRNAs via known protein structural motifs. One of these is the oligonucleotide/oligosaccharide-binding (OB)-fold that has a highly conserved β-barrel structure found in organisms across all domains of life. However, the details of its interactions with tRNA are not completely understood. Recent research from a team at the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) has provided new, previously unrecognized, insights into how the OB-fold recognizes the 3’ tail of tRNA molecules and how these interactions impact the function of tRNAs.
The research team used X-ray diffraction data collected at the South East Regional Collaborative Access Team (SER-CAT) beamline 22-ID of the Advanced Photon Source, a U.S. Department of Energy (DOE) user facility at DOE’s Argonne National Laboratory.
The protein structure work in this project focused on a superfamily of proteins called the tRNA binding domain (TRBD) family. These proteins interact with tRNAs via an OB-fold domain that consists of five β strands that form a barrel structure with an α-helical cap. TRBD proteins are found in many different organisms and, while they don’t always have high levels of amino acid sequence conservation, they all contain the OB-fold.
This work started with a TRBD protein from the bacteria Aquifex aeolicus called Trbp111 that is known to bind to many tRNAs. Solution of a new 2.3 Å crystal structure of Trbp111 showed that the protein forms an unusually stable homodimer with the two β-barrels stabilized by a very strong dimer interface. This is consistent with what is known about Trbp111, as A. aeolicus thrives at high temperatures (~90°C) and is also resistant to many common laboratory protein denaturing procedures, suggesting that this type of stable interface may provide a model for artificial protein design and structure-based drug design efforts.
Read more on Argonne website
Image: The figure shows how the OB beta barrel uses its two protruding loops as “pincers” to capture the terminal CA dinucleotide of the tRNA in various representations (tRNAs are shown in green in each panel).