Transfer RNA tour: Difference between revisions

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The acceptor stem includes the 5' and 3' ends of the tRNA. The 5' end is generated by RNaseP :-). The 3' end is the site which is charged with amino acids for translation. Some aminoacyl tRNA synthetases interact with both the acceptor 3' end and

the anticodon when charging tRNAs. Note how far the 3' end is from the anticodon loop, at bottom, by clicking here. Note also how the acceptor stem stacks onto the TpsiC stem to form a continuous helix. The anticodon stem also stacks onto the junction between the variable loop and the D stem to form another nearly perfect helix. The TpsiC and D loops interact to bring the "cloverleaf" secondary structure in to the L-shaped tertiary structure.

the anticodon when charging tRNAs. <scene name='72/725890/Trna_overview/2'>Note how far the 3' end is</scene> from the anticodon loop, at bottom, by clicking here. Note also how the acceptor stem stacks onto the TpsiC stem to form a continuous helix. The anticodon stem also stacks onto the junction between the variable loop and the D stem to form another nearly perfect helix. The TpsiC and D loops interact to bring the "cloverleaf" secondary structure in to the L-shaped tertiary structure.

===Core Tertiary Interactions===

Now <scene name='72/725890/Trna_tert_interact/1'> highlight the tertiary interactions</scene>.

Most of the backbone is shown in ribbon format, with the same color scheme as above. Several unusual base pairs, base triples and turns are highlighted and color-coded.

[[Image:JnTerts.GIF]]

The yellow residues are a parallel base pair (compared to the normal anti parallel) between G15 of the D-loop and C48 of the variable loop. This brings the D-loop and variable loop together. Note the sharp turn in the backbone between C48 and C49 caused by the parallel pair.

<scene name='72/725890/Trna_tert_interact/2'>You can zoom in for a closer look</scene>. The yellow residues are a parallel base pair (compared to the normal anti parallel) between G15 of the D-loop and C48 of the variable loop. This brings the D-loop and variable loop together. Note the sharp turn in the backbone between C48 and C49 caused by the parallel pair.

The green residues are a reverse Hoogsteen pair between U8and A14. This pairing is important for positioning of the D stem relative to the stacked T and acceptor stems.

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 The <B><FONT COLOR="#0000ff">acceptor stem</FONT></B> includes the 5' and 3' ends of the tRNA. The 5' end is generated by RNaseP :-). The 3' end is the site which is charged with amino acids for translation. Some aminoacyl tRNA synthetases interact with both the <B><FONT COLOR="#0000ff">acceptor</FONT></B> 3' end and
-the <B><FONT COLOR="#ff0000">anticodon</FONT></B> when charging tRNAs. Note how far the 3' end is from the <B><FONT COLOR="#ff0000">anticodon loop</FONT></B>, at bottom, by clicking here. Note also how the <B><FONT COLOR="#0000ff">acceptor stem</FONT></B> stacks onto the <B><FONT COLOR="#008aff">TpsiC stem</FONT></B> to form a continuous helix. The <B><FONT COLOR="#ff0000">anticodon stem</FONT></B> also stacks onto the junction between the <B><FONT COLOR="#aaaa00">variable loop</FONT></B> and the <B><FONT COLOR="#ff00ff">D stem</FONT></B> to form another nearly perfect helix. The <B><FONT COLOR="#008aff">TpsiC</FONT></B> and <B><FONT COLOR="#ff00ff">D loops</FONT></B> interact to bring the &quot;cloverleaf&quot; secondary structure in to the L-shaped tertiary structure.
+the <B><FONT COLOR="#ff0000">anticodon</FONT></B> when charging tRNAs. <scene name='72/725890/Trna_overview/2'>Note how far the 3' end is</scene> from the <B><FONT COLOR="#ff0000">anticodon loop</FONT></B>, at bottom, by clicking here. Note also how the <B><FONT COLOR="#0000ff">acceptor stem</FONT></B> stacks onto the <B><FONT COLOR="#008aff">TpsiC stem</FONT></B> to form a continuous helix. The <B><FONT COLOR="#ff0000">anticodon stem</FONT></B> also stacks onto the junction between the <B><FONT COLOR="#aaaa00">variable loop</FONT></B> and the <B><FONT COLOR="#ff00ff">D stem</FONT></B> to form another nearly perfect helix. The <B><FONT COLOR="#008aff">TpsiC</FONT></B> and <B><FONT COLOR="#ff00ff">D loops</FONT></B> interact to bring the &quot;cloverleaf&quot; secondary structure in to the L-shaped tertiary structure.
 ===Core Tertiary Interactions===
 Now <scene name='72/725890/Trna_tert_interact/1'> highlight the tertiary interactions</scene>.
 Most of the backbone is shown in ribbon format, with the same color scheme as above. Several unusual base pairs, base triples and turns are highlighted and color-coded.
 [[Image:JnTerts.GIF]]
-The yellow residues are a parallel base pair (compared to the normal anti parallel) between <B><FONT COLOR="#ffff00">G15</FONT></B> of the <B>D-loop</B> and <B><FONT COLOR="#ffff00">C48</FONT></B> of the <B>variable loop</B>. This brings the <B>D-loop</B> and <B>variable loop</B> together. Note the sharp turn in the backbone between <B><FONT COLOR="#ffff00">C48</FONT></B> and <B><FONT COLOR="#ffff00">C49</FONT></B> caused by the parallel pair.</P>
+<scene name='72/725890/Trna_tert_interact/2'>You can zoom in for a closer look</scene>. The yellow residues are a parallel base pair (compared to the normal anti parallel) between <B><FONT COLOR="#aaaa00">G15</FONT></B> of the <B>D-loop</B> and <B><FONT COLOR="#aaaa00">C48</FONT></B> of the <B>variable loop</B>. This brings the <B>D-loop</B> and <B>variable loop</B> together. Note the sharp turn in the backbone between <B><FONT COLOR="#ffff00">C48</FONT></B> and <B><FONT COLOR="#ffff00">C49</FONT></B> caused by the parallel pair.</P>
 The green residues are a reverse Hoogsteen pair between <B><FONT COLOR="#00bf00">U8</FONT></B>and <B><FONT COLOR="#00bf00">A14</FONT></B>. This pairing is important for positioning of the <B>D stem</B> relative to the stacked <B>T</B> and <B>acceptor</B> stems.</P>