Transfer RNA tour: Difference between revisions

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==tRNA==

Source <ref>PMID:790568</ref>

== Structural highlights ==

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[[Image:JnTerts.GIF]]

<scene name='72/725890/Trna_tert_interact/7'>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.

<scene name='72/725890/Trna_tert_interact/8'>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 U8 and A14. This pairing is important for positioning of the D stem relative to the stacked T and acceptor stems.

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The red residues are a base triple in which 7-methyl-G46 from the variable loop H-bonds to the G22-C13 base pair of the D stem. This helps dock the variable loop onto the D-stem.

A9 is also involved in another type of tertiary interaction: it is <scene name='72/725890/Trna_tertwire/2'>intercalated between bases</scene> 7-methyl-G46 and G45. In order to make room between these bases for A9 the backbone is extended by a C2' endo sugar pucker at 7-methyl-G46.

A9 is also involved in another type of tertiary interaction: it is <scene name='72/725890/Trna_tertwire/3'>intercalated between bases</scene> 7-methyl-G46 and G45. In order to make room between these bases for A9 the backbone is extended by a C2' endo sugar pucker at 7-methyl-G46.

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@@ Line 1: / Line 1: @@
 ==tRNA==
-<StructureSection load='1tra' size='400' side='right' caption='phe-tRNA [[1tra]]' scene='72/725890/Trna_overview/1'>
+<StructureSection load='1tra' size='350' side='right' caption='phe-tRNA [[1tra]]' scene='72/725890/Trna_overview/1'>
 Source <ref>PMID:790568</ref>
 == Structural highlights ==
@@ Line 15: / Line 15: @@
 [[Image:JnTerts.GIF]]
-<scene name='72/725890/Trna_tert_interact/7'>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="#aaaa00">C48</FONT></B> and <B><FONT COLOR="#aaaa00">C49</FONT></B> caused by the parallel pair.
+<scene name='72/725890/Trna_tert_interact/8'>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="#aaaa00">C48</FONT></B> and <B><FONT COLOR="#aaaa00">C49</FONT></B> caused by the parallel pair.
 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.
@@ Line 23: / Line 23: @@
 The red residues are a base triple in which <B><FONT COLOR="#ff0000">7-methyl-G46</FONT></B> from the <B>variable loop</B> H-bonds to the <B><FONT COLOR="#ff0000">G22-C13</FONT></B> base pair of the <B>D stem</B>. This helps dock the <B>variable loop</B> onto the <B>D-stem</B>.
-<B><FONT COLOR="#008aff">A9</FONT></B> is also involved in another type of tertiary interaction: it is <scene name='72/725890/Trna_tertwire/2'>intercalated between bases</scene> <B><FONT COLOR="#ff0000">7-methyl-G46</FONT></B> and <B>G45</B>. In order to make room between these bases for <B><FONT COLOR="#008aff">A9</FONT></B> the backbone is extended by a C2' endo sugar pucker at <B><FONT COLOR="#ff0000">7-methyl-G46</FONT></B>.
+<B><FONT COLOR="#008aff">A9</FONT></B> is also involved in another type of tertiary interaction: it is <scene name='72/725890/Trna_tertwire/3'>intercalated between bases</scene> <B><FONT COLOR="#ff0000">7-methyl-G46</FONT></B> and <B>G45</B>. In order to make room between these bases for <B><FONT COLOR="#008aff">A9</FONT></B> the backbone is extended by a C2' endo sugar pucker at <B><FONT COLOR="#ff0000">7-methyl-G46</FONT></B>.