Proteopedia

Transfer RNA tour: Difference between revisions

← Older edit
mNo edit summary
No edit summary
 
(16 intermediate revisions by 2 users not shown)
Line 1: Line 1:
==A-form RNA==
==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:77038371</ref>
Source <ref>PMID:790568</ref>
== Structural highlights ==
== Structural highlights ==
===Domains===
===Domains===
Line 10: Line 10:
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.
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===
===Core Tertiary Interactions===
Now <scene name='72/725890/Trna_tert_interact/1'> highlight the tertiary interactions</scene>.
Now <scene name='72/725890/Trna_tert_interact/6'> 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.
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]]
[[Image:JnTerts.GIF]]


<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>
<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.</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.


The cyan residues are a base triple in which <B><FONT COLOR="#008aff">A9</FONT></B>H-bonds in the major groove to <B><FONT COLOR="#008aff">A23</FONT></B> (which is paired with <B><FONT COLOR="#008aff">U12</FONT></B>). It stabilizes a sharp turn between bases 9 and 10.</P>
The cyan residues are a base triple in which <B><FONT COLOR="#008aff">A9</FONT></B> H-bonds in the major groove to <B><FONT COLOR="#008aff">A23</FONT></B> (which is paired with <B><FONT COLOR="#008aff">U12</FONT></B>). It stabilizes a sharp turn between bases 9 and 10.


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>.</P>
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/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===
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">&quot;T-loop&quot;</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.
</StructureSection>
==See Also==
* [[Z-DNA model tour]] and [[Z-DNA]]
* [[B-DNA tour]]
* [[A-RNA tour]]
* A more general overview will be found at [[DNA]].
* [[Forms of DNA]] shows a side-by-side comparison of A, B, and Z forms of DNA.
* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.


== References ==
== References ==

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

James Nolan, Michal Harel
Retrieved from "https://proteopedia.openfox.io/w/Transfer_RNA_tour"