Domain structure of class II tRNA synthetases

In this section you will study the similarity between functional domains in tRNA synthetases from two domains of life.

In the following steps, we will perform a search for the tRNA synthetases from E. coli and M. jannaschii in a database that can perform searches based on similar domain structure, the NCBI Entrez Structure/MMDB/3D Domain tools. Sample output is shown in Figure 1.

• At the home page of the NCBI database (http://www.ncbi.nlm.nih.gov), set the search-type pop-up menu to Structure and search for tRNA synthetase.

• In the search result lists, click on the links for the individual tRNA synthetases (e.g. 1NJ5) to access information about the domain structure of individual class II tRNA synthetases. Click on individual domains in the 3D Domain to see a display of structural neighbors: domains with similar structure to your target domain are shown aligned to your target domain. (Warning: if you receive the error ``Vast neighbor data for this domain are not yet available.'', just use the Back button to return to the search results and try again with another structure.)

• The online web version of this tutorial includes a color figure of the domains of tRNA synthetase, color-coded by domain as Figure 1. The NCBI domain results are colored by the same code as in this figure: magenta= Catalytic, blue= Insert I, orange= Insert II, green = Anticodon.

• Look among the entires in your search results to find tRNA synthetases from two or three different species. Open separate browser windows to show the domain organization of each and compare their 1-D organization.

• Look among the entires in your search results to find two or three tRNA synthetases from the same species. Open separate browser windows to show the domain organization of each and compare their 1-D organization.

Figure 1: Domains of Glutamine aminoacyl-tRNA synthetase. The bound tRNA is shown with red backbone on the right side of the figure.