Transfer RNA tour: Difference between revisions
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==tRNA== | ==tRNA== | ||
<StructureSection load='1tra' size=' | <StructureSection load='1tra' size='350' side='right' caption='phe-tRNA [[1tra]]' scene='72/725890/Trna_overview/1'> | ||
Source <ref>PMID:790568</ref> | Source <ref>PMID:790568</ref> | ||
== Structural highlights == | == Structural highlights == | ||
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[[Image:JnTerts.GIF]] | [[Image:JnTerts.GIF]] | ||
<scene name='72/725890/Trna_tert_interact/ | <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. | 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. | ||
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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>. | 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/ | <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>. | ||
===U-turns=== | ===U-turns=== | ||
The <scene name='72/725890/Trna_u--turn/1'>conserved ''U-turn'' motifs</scene> are responsible for turns in the <B><FONT COLOR="#ff0000">anticodon</FONT></B> and <B><FONT COLOR="#008aff">T</FONT></B> loops. The turn is stabilized by an H-bond between a conserved U residue and the phosphate backbone and an H-bond fron the O2' of the U to the N7 of a conserved purine. <scene name='72/725890/Trna_u--turn/ | The <scene name='72/725890/Trna_u--turn/1'>conserved ''U-turn'' motifs</scene> are responsible for turns in the <B><FONT COLOR="#ff0000">anticodon</FONT></B> and <B><FONT COLOR="#008aff">T</FONT></B> loops. The turn is stabilized by an H-bond between a conserved U residue and the phosphate backbone and an H-bond fron the O2' of the U to the N7 of a conserved purine. <scene name='72/725890/Trna_u--turn/8'>Zoom in on the anticodon-loop U-turn</scene>. Residues <B><FONT COLOR="#ff0000">33-35</FONT></B> form the <B>U-turn</B>, N3 of <B><FONT COLOR="#ff0000">U33</FONT></B> H-bonds to the phosphate oxygen of <B><FONT COLOR="#ff00ff">A36</FONT></B>, the O2' of <B><FONT COLOR="#ff0000">U33</FONT></B> H-bonds to the N7 of <B><FONT COLOR="#ff0000">A35</FONT></B>. Residues <B><FONT COLOR="#ff0000">34</FONT></B>, <B><FONT COLOR="#ff0000">35</FONT></B> and <B><FONT COLOR="#ff00ff">36</FONT></B> are the anticodon bases used in translation. The hypermodified wybutrosine <B><FONT COLOR="#aaaa00">YG37</FONT></B> is believed to form a steric block to frameshifting during translation. | ||
The ''U-turn'' motif is repeated in the <B><FONT COLOR="#008aff">"T-loop"</FONT></B> of tRNA. <scene name='72/725890/Trna_u--turn/6'>Zoom in on the T-loop U-turn</scene>. Residues <B><FONT COLOR="#008aff">55-57</FONT></B> form the U-turn here. A <B>U-turn</B> is also found in the active site of the hammerhead ribozyme. | The ''U-turn'' motif is repeated in the <B><FONT COLOR="#008aff">"T-loop"</FONT></B> of tRNA. <scene name='72/725890/Trna_u--turn/6'>Zoom in on the T-loop U-turn</scene>. Residues <B><FONT COLOR="#008aff">55-57</FONT></B> form the U-turn here. A <B>U-turn</B> is also found in the active site of the hammerhead ribozyme. | ||