2lbr: Difference between revisions

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[[Image:2lbr.png|left|200px]]


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==Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR==
The line below this paragraph, containing "STRUCTURE_2lbr", creates the "Structure Box" on the page.
<StructureSection load='2lbr' size='340' side='right'caption='[[2lbr]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2lbr]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LBR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
{{STRUCTURE_2lbr|  PDB=2lbr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lbr OCA], [https://pdbe.org/2lbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lbr RCSB], [https://www.ebi.ac.uk/pdbsum/2lbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lbr ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
tRNA molecules contain 93 chemically unique nucleotide base modifications that expand the chemical and biophysical diversity of RNA and contribute to the overall fitness of the cell. Nucleotide modifications of tRNA confer fidelity and efficiency to translation and are important in tRNA-dependent RNA-mediated regulatory processes. The three-dimensional structure of the anticodon is crucial to tRNA-mRNA specificity, and the diverse modifications of nucleotide bases in the anticodon region modulate this specificity. We have determined the solution structures and thermodynamic properties of Bacillus subtilis tRNA(Tyr) anticodon arms containing the natural base modifications N(6)-dimethylallyl adenine (i(6)A(37)) and pseudouridine (psi(39)). UV melting and differential scanning calorimetry indicate that the modifications stabilize the stem and may enhance base stacking in the loop. The i(6)A(37) modification disrupts the hydrogen bond network of the unmodified anticodon loop including a C(32)-A(38)(+) base pair and an A(37)-U(33) base-base interaction. Although the i(6)A(37) modification increases the dynamic nature of the loop nucleotides, metal ion coordination reestablishes conformational homogeneity. Interestingly, the i(6)A(37) modification and Mg(2+) are sufficient to promote the U-turn fold of the anticodon loop of Escherichia coli tRNA(Phe), but these elements do not result in this signature feature of the anticodon loop in tRNA(Tyr).


===Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR===
Conformation Effects of Base Modification on the Anticodon Stem-Loop of Bacillus subtilis tRNA(Tyr).,Denmon AP, Wang J, Nikonowicz EP J Mol Biol. 2011 Sep 16;412(2):285-303. Epub 2011 Jul 19. PMID:21782828<ref>PMID:21782828</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_21782828}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2lbr" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 21782828 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_21782828}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2lbr]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBR OCA].
[[Category: Denmon AP]]
 
[[Category: Nikonowicz EP]]
==Reference==
[[Category: Wang J]]
<ref group="xtra">PMID:021782828</ref><references group="xtra"/>
[[Category: Denmon, A P.]]
[[Category: Nikonowicz, E P.]]
[[Category: Wang, J.]]
[[Category: Rna]]
[[Category: Tyrosyl-trna]]

Latest revision as of 05:41, 15 May 2024

Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR

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