Transfer RNA tour: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 4: Line 4:
== Structural highlights ==
== Structural highlights ==
===Domains===
===Domains===
<scene name='72/725890/Trna_tertcolor/3'>Color the tRNA 3D structure to match the secondary structure below</scene>.
[[Image:JnTphe.GIF]]
[[Image:JnTphe.GIF]]
<scene name='72/725890/Trna_tertcolor/3'>Color the tRNA 3D structure to match the secondary structure above</scene>.


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="#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. 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.
===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]]


<scene name='72/725890/Trna_tert_interact/1'>TextToBeDisplayed</scene>
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>
The tour starts with the <scene name='72/725869/A-rna_overview/1'>Default</scene> view. Now look at this <scene name='72/725869/Rna_space_filling_view/2'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (at the top, when you have just clicked the button) is very deep.


Now change the display to make the show the <scene name='72/725869/Rna_space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other but not perpendicular to the axis of the double helix. They are also displaced to the side of the axis. The result is a wide, short helix. Note also that the backbone forms a smooth, continuous curve.
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 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 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>


You can <scene name='72/725869/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725869/Zoom_pairs_only/1'>look at just the bases</scene>.
Each base pair stacks on the next similarly, as shown from <scene name='72/725869/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725869/Zoom_pairs_only_top/1'>same top view of just the bases</scene>. 
B-DNA stacks similarly, but compare this with Z-DNA, which behaves much differently.  Essentially all helical RNA is in A form, but DNA can also be found in A form under certain conditions (particularly in RNA-DNA hybrids). The 2'-OH of ribose  favors the C3'-''endo'' sugar pucker necessary for A-form geometry. The O2' is easily seen as white spheres in <scene name='72/725869/Rna_space_filling_o2prime/1'>this space fill view</scene>.


You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stereo picture of A, B, and Z DNA]
</StructureSection>
==See Also==
* [[Z-DNA model tour]] and [[Z-DNA]]
* [[B-DNA 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 ==


Revision as of 19:57, 25 February 2016

A-form RNAA-form RNA

<StructureSection load='1tra' size='400' side='right' caption='phe-tRNA 1tra' scene='72/725890/Trna_overview/1'> Source [1]

Structural highlightsStructural highlights

DomainsDomains

.

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.

Core Tertiary InteractionsCore Tertiary Interactions

Now . 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.

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.

The cyan residues are a base triple in which A9H-bonds in the major groove to A23 (which is paired with U12). It stabilizes a sharp turn between bases 9 and 10.

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.


ReferencesReferences

JSmol in Proteopedia [2] or to the article describing Jmol [3] to the rescue.


  1. ↑ . PMID:77038371
  2. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  3. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

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/wiki/index.php?title=Transfer_RNA_tour&oldid=2575292"