Yeast Phenylalanine tRNA

A tutorial by by Steve Minchin, University of Birmingham

General Information

To view the tRNA molecule on the right you require the Chemscape Chime plug-in with NetScape or Microsoft® Internet Explorer (requires Chime 2.0). If you can see the tRNA molecule then you are ready to view the tutorial. The plug-in can be downloaded from MDL Information Systems, Inc.

On the right is the structure of yeast phenylalanine tRNA taken from 6tna.pdb Sussman,J.L., Holbrook,S.R., Warrant,R.W., Church,G.M. and Kim,S.-H. (1978) J. Mol. Biol. 123:607-630.
At any time you can reset the model by clicking this button .

To manipulate the model press and hold the left hand mouse button and drag to obtain the desired view. To zoom press the shift key and left mouse button while moving the mouse. To move position of the molecule press the Ctrl key and the right mouse button while moving the mouse. To alter the presentation of the image or stop the rotation click with the right hand mouse button and select one of the options.

Notes: Hydrogen atoms are not displayed hence hydrogen bonds will not be displayed even when the option is selected.

The Tutorial

The original view shows the tRNA with the atoms coloured as follows; Carbon - grey, Oxygen - red, Nitrogen - light blue, Hydrogen - white and phosphorous - orange. The model is displayed in the stick form to show the bonds between atoms. A more realistic representation of the tRNA is the spacefilling model ; here, the size of each molecule is represented by its bonding properties and van der Waals radius.

Yeast phenylalanine tRNA is the adaptor molecule which puts Phe into proteins. The codons for phe are UUU and UUC. For this tRNA the anticodon is GAA and is located in the anticodon loop . To perform its function tRNAphe must first be attached to (charged with) phenylalanine. The enzyme aminoacyl-tRNA synthetase attaches phe at the end of the amino acid acceptor stem . The charged tRNA then interacts with the messenger RNA at the surface of the ribosome. tRNAs fold into a common, L-shaped, three dimensional structure refered to as a clover leaf (see diagram below).

This structure contains three "leaves" (the anticodon loop , the D loop and the tyc loop ) and a fourth variably sized loop . Regions between loops are refered to as stems. The anticodon and D stems fold into a helix as do the tyc and acceptor stems . The tRNA contains several modified nucleotides .
Interactions between the variable loop and the D stem (red) and between the D and Tyc (cyan) loops are important for maintaining the L-shape fold of the tRNA (detailed view ). The loops and the regions of helical conformation are clearly important for the specific interactions the tRNA must make with the aminoacyl-tRNA synthetase and the messenger RNA and ribosome.

Further information about the structure of yeast phenylalanine tRNA can be found in Rich,A. & Kim,S.H. (1978) The three-dimensional structure of transfer RNA Scientific American 238:52-62. This includes a discussion about how the structure is stabilised by non Watson-Crick base-pairing which has not been discussed in this tutorial.

Action

Cartoon

Detail

Reset

Spacefill

Show amino acid attachment site

Show anticodon

Zoom in on anticodon

Show Amino Acid acceptor stem

Show D Stem

Show D loop

Show Anticodon Stem

Show Anticodon loop

Show Variable loop

Show TyC Stem

Show TyC loop

Show all three loops

Show Anticodon and D stems

Show TyC and amino acid acceptor stems

Show modified bases

Action	Cartoon	Detail
Reset
Spacefill
Show amino acid attachment site
Show anticodon
Zoom in on anticodon
Show Amino Acid acceptor stem
Show D Stem
Show D loop
Show Anticodon Stem
Show Anticodon loop
Show Variable loop
Show TyC Stem
Show TyC loop
Show all three loops
Show Anticodon and D stems
Show TyC and amino acid acceptor stems
Show modified bases