Transfer RNA tour: Difference between revisions
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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/5'>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. | ||
Revision as of 01:03, 28 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. 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 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.
U-turnsU-turns
The 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.
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