Transfer RNA tour: Difference between revisions
James Nolan (talk | contribs) mNo edit summary |
James Nolan (talk | contribs) No edit summary |
||
| (16 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
== | ==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: | 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 "cloverleaf" 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 "cloverleaf" secondary structure in to the L-shaped tertiary structure. | ||
===Core Tertiary Interactions=== | ===Core Tertiary Interactions=== | ||
Now <scene name='72/725890/Trna_tert_interact/ | 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/ | <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. | ||
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 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>. | 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">"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. | |||
</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 == | ||
Latest revision as of 17:25, 24 September 2019
tRNAtRNA
Source [1] Structural highlightsDomains.
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. 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 InteractionsNow . 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 U8 and 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 A9 H-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. A9 is also involved in another type of tertiary interaction: it is 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.
U-turnsThe are responsible for turns in the anticodon and T 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. . Residues 33-35 form the U-turn, N3 of U33 H-bonds to the phosphate oxygen of A36, the O2' of U33 H-bonds to the N7 of A35. Residues 34, 35 and 36 are the anticodon bases used in translation. The hypermodified wybutrosine YG37 is believed to form a steric block to frameshifting during translation. The U-turn motif is repeated in the "T-loop" of tRNA. . Residues 55-57 form the U-turn here. A U-turn is also found in the active site of the hammerhead ribozyme. |
| ||||||||||
See AlsoSee 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 DNA Structure, disponible también en español and eight other languages.
ReferencesReferences
JSmol in Proteopedia [2] or to the article describing Jmol [3] to the rescue.
- ↑ Quigley GJ, Rich A. Structural domains of transfer RNA molecules. Science. 1976 Nov 19;194(4267):796-806. PMID:790568
- ↑ 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
- ↑ 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