The Aspartyl-tRNA Synthetase Aspartyl-adenylate Complex

In order to become familiar with the structural and functional features of the AARSs, we will first explore the aspartyl-tRNA synthetase as complexed with aspartyl-adenylate and tRNA (PDB code: 1C0A). To do this:

1 Go to the terminal window.

2 At the prompt type: > source trna.vmd.

You should now have the AspRS-tRNA aspartyl-adenylate complex loaded in VMD. Take some time to explore the complex in the Open GL display; rotate the molecule; investigate the different features and components of the complex, including the location of substrates and the way tRNA is positioned in complex with the AspRS. Note that the tRNA makes contact with the synthetase in several locations.

All of the AARSs are multidomain proteins, but the exact number and fold of each domain is specific to each aminoacyl-tRNA synthetase. AspRS has a catalytic domain (shown in blue), an anticodon binding domain (orange, sometimes also referred to as the N-terminal domain), and an insertion domain (shown in pink). Curiously, the insertion domain (residues 288 to 420) literally interrupts the sequence of the catalytic domain (comprised of residues 113 to 287 and 421 to 585) and only appears in the bacterial AspRS; archaea and eukarya AspRSs do not contain this insertion.

Note how the N-terminal domain (colored orange) of the enzyme attaches itself to the anticodon in the tRNA; zoom in on the anticodon. The anticodon for aspartate is comprised of Q34, U35, and C36. Q stands for queuine and is a hypermodified base that marks the first position of the anticodon in the AARSs that code for Asp, Asn, His, and Tyr.

Use VMD to zoom in on the active site within the catalytic domain; you may want to rotate the molecule to get the best view possible. Note how the acceptor end of the tRNA sticks into the active site of the aspartyl synthetase. The substrate, aspartyl-adenylate, is shown in space-filling representation. The formation of the aspartyl-adenylate comes from one aspartate molecule and ATP; this adenylated species is "activated" and from here can easily be linked to the cognate tRNA with energy provided from the hydrolysis of ADP to AMP. Also note how the architecture of the active site prohibits the diffusion of this activated amino acid outside of the active site; the aspartyl-adenylate is trapped between the catalytic domain and the tRNA.

Send the tRNA off to the ribosome yourself by deleting the molecule before you begin the next part of the tutorial.
 
In the subsequent parts of this tutorial, we will use MultiSeq to align the catalytic domains of three AspRS molecules, one from each of the domains of life, as well as one serine tRNA synthetase. The catalytic domain of each species has been directly extracted from the ASTRAL database, which contains the structures of each of the proteins' domains. This tutorial will emphasize both structural and sequence-based analyses of the AARSs and ultimately create a phylogenetic tree illustrating the evolution of the proteins with respect to one another. For a more thorough explanation of the evolutionary considerations, as well as the computational methods involved, please see Ref. 1.