2lbq: Difference between revisions
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<StructureSection load='2lbq' size='340' side='right' caption='[[2lbq]], [[NMR_Ensembles_of_Models | 8 NMR models]]' scene=''> | <StructureSection load='2lbq' size='340' side='right' caption='[[2lbq]], [[NMR_Ensembles_of_Models | 8 NMR models]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2lbq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBQ OCA]. <br> | <table><tr><td colspan='2'>[[2lbq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LBQ FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2lbr|2lbr]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2lbr|2lbr]]</td></tr> | ||
<tr | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lbq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lbq RCSB], [http://www.ebi.ac.uk/pdbsum/2lbq PDBsum]</span></td></tr> | ||
</table> | |||
<table> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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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> | 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 | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
== References == | == References == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: Denmon, A P | [[Category: Denmon, A P]] | ||
[[Category: Nikonowicz, E P | [[Category: Nikonowicz, E P]] | ||
[[Category: Wang, J | [[Category: Wang, J]] | ||
[[Category: Rna]] | [[Category: Rna]] | ||
[[Category: Tyrosyl-trna]] | [[Category: Tyrosyl-trna]] | ||
Revision as of 08:43, 22 December 2014
NMR structure of i6A37_tyrASLNMR structure of i6A37_tyrASL
Structural highlights
Publication Abstract from PubMedtRNA 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 tRNA(Tyr).,Denmon AP, Wang J, Nikonowicz EP J Mol Biol. 2011 Sep 16;412(2):285-303. Epub 2011 Jul 19. PMID:21782828[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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