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Glutaminyl-tRNA Synthetase


Protein Representation:
tRNA Representation:
Hi-lite Interface:

ATP:

Aspartyl tRNA Synthetase


Protein Representation:
tRNA Representation:
Hi-lite Interface:

ATP:
Learning Objectives
  1. To understand that an aminoacyl-tRNA synthetase contacts its tRNA at several points.
  2. To understand that synthetases interact with the major or minor groove of the tRNA acceptor stem.
  3. To understand that the two classes of synthetase aminoacylate different atoms on the tRNA's 5´-terminal residue.

Activity Instructions

Compare the 3D structures of these two aminoacyl–tRNA synthetases. Each has its corresponding tRNA bound to it, as well as a bound ATP molecule. The first complex shown is that of glutaminyl–tRNA synthetase (GlnRS) from E. coli, and the second complex is aspartyl–tRNA synthetase (AspRS) from yeast. The ATPs are shown in space-filling mode. The tRNA may be alternatively displayed in 'Ball & Stick' form and 'CPK' (space-filling) form, and the protein may be alternatively displayed in 'CPK' and 'Cartoon' (ribbon) form. Toggle the "Hi-lite Protein" button in the Interface section of the control panel to color the protein residues in contact with the tRNA green and the "Hi-lite tRNA" button to color the tRNA residues in contact with the protein yellow.


Questions
  1. What portion of the tRNA does NOT make contact with the protein? Answer
  2. In what portions of the tRNA are nucleotides 11, 35, 56 and 73 located? Answer
  3. What are the identities of the bases at positions 11, 35, 56 and 73 in GlnRS? In AspRS? Answer
  4. What is the conformation (A, B or Z) of the acceptor stem? Answer
  5. What structural aspects of the major and minor grooves of a tRNA allows their identification? Which, if any, of the aminoacyl–tRNA synthetases bind to the major groove of its cognate tRNA's acceptor stem? Which, if any, bind to the acceptor stem's minor groove? [Note. A tRNA's grooves are most easily visually differentiated when the tRNA is displayed in CPK form and rotated about.] Answer
  6. A Class I aminoacyl–tRNA synthetase (aaRS) aminoacylates the 2'-OH group of its cognate tRNA's 5'-terminal A residue, whereas a Class II aaRS aminoacylates the corresponding 3'-OH group. By zooming into the active site region of each tRNA (the region around the ATP's α-phosphorous atom) and comparing the relative dispositions of O2' and O3' on the tRNA's 5'-terminal A residue with respect to the ATP's α-phosphorus atom, determine the class of GlnRS and AspRS. Answer