SCOP fold classification

As with all multi-domain proteins, the properties of Class II tRNA synthetases depend on their component domains. The schematic domain structure of aspartyl class II tRNA synthetase from Eubacteria is depicted in Figure 1.

Only one domain is common to all class II tRNA synthetases studied so far: the catalytic domain, which carries out the amino acid loading reaction. In later sections of this tutorial, you will align the catalytic domains of class II tRNA synthetases using Needleman-Wunsch sequence alignment, and with structure-based alignment methods. The fourth column of Table 6 provide you with the ASTRAL database accession codes [6]. The ASTRAL database (http://astral.stanford.edu) is a compendium of protein domain structures derived from the PDB database  [7].

In the following exercise you will classify one of your chosen catalytic domains in folds, superfamilies and families with help of the database SCOP (Structural Classification Of Proteins) [8].

• Point your web browser to the SCOP server (http://scop.berkeley.edu/index.html).

• You are going to browse a hierarchy of protein structural classifications. Go to the top of the hierarchy: Click on the link top of the hierarchy. This places you at the root of all the protein classes deposited in SCOP.

• Click on one of the Classes links (e.g. Alpha and Beta proteins); you should reach the next hierarchy level of folds. Note how lineage records your path through the hierarchy.

• Some of the entries have pre-prepared 3D structure renderings of an example of the protein class. Click on the purple and white buttons to the right of a few entries to see an example view of the chosen protein class.

• We will now search for entries relevant to a particular domain of interest. Now enter one of the ASTRAL database catalytic domain codes from Table 6 (e.g. d1asza2) in the Search field you find at the bottom of the page.

• You should reach a window showing the SCOP lineage and a summary of all relevant PDB entry domains. For subsequent exercises we have provided you with catalytic domain coordinates of Class II tRNA synthetases obtained from the ASTRAL database. The ASTRAL coordinate files are produced by extracting domains from PDB coordinate files.