1f1t
From Proteopedia
(New page: 200px<br /><applet load="1f1t" size="450" color="white" frame="true" align="right" spinBox="true" caption="1f1t, resolution 2.8Å" /> '''CRYSTAL STRUCTURE OF ...) |
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| - | [[Image:1f1t.gif|left|200px]]<br /><applet load="1f1t" size=" | + | [[Image:1f1t.gif|left|200px]]<br /><applet load="1f1t" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1f1t, resolution 2.8Å" /> | caption="1f1t, resolution 2.8Å" /> | ||
'''CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE'''<br /> | '''CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Previous in vitro selection experiments identified an RNA aptamer that | + | Previous in vitro selection experiments identified an RNA aptamer that recognizes the chromophore malachite green (MG) with a high level of affinity, and which undergoes site-specific cleavage following laser irradiation. To understand the mechanism by which this RNA folds to recognize specifically its ligand and the structural basis for chromophore-assisted laser inactivation, we have determined the 2.8 A crystal structure of the aptamer bound to tetramethylrosamine (TMR), a high-affinity MG analog. The ligand-binding site is defined by an asymmetric internal loop, flanked by a pair of helices. A U-turn and several non-canonical base interactions stabilize the folding of loop nucleotides around the TMR. The aptamer utilizes several tiers of stacked nucleotides arranged in pairs, triples, and a novel base quadruple to effectively encapsulate the ligand. Even in the absence of specific stabilizing hydrogen bonds, discrimination between related fluorophores and chromophores is possible due to tight packing in the RNA binding pocket, which severely limits the size and shape of recognized ligands. The site of laser-induced cleavage lies relatively far from the bound TMR ( approximately 15 A). The unusual backbone conformation of the cleavage site nucleotide and its high level of solvent accessibility may combine to allow preferential reaction with freely diffusing hydroxyl radicals generated at the bound ligand. Several observations, however, favor alternative mechanisms for cleavage, such as conformational changes in the aptamer or long-range electron transfer between the bound ligand and the cleavage site nucleotide. |
==About this Structure== | ==About this Structure== | ||
| - | 1F1T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with SR and ROS as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1F1T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SR:'>SR</scene> and <scene name='pdbligand=ROS:'>ROS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F1T OCA]. |
==Reference== | ==Reference== | ||
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[[Category: u-turn]] | [[Category: u-turn]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:33:53 2008'' |
Revision as of 10:33, 21 February 2008
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CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE
Overview
Previous in vitro selection experiments identified an RNA aptamer that recognizes the chromophore malachite green (MG) with a high level of affinity, and which undergoes site-specific cleavage following laser irradiation. To understand the mechanism by which this RNA folds to recognize specifically its ligand and the structural basis for chromophore-assisted laser inactivation, we have determined the 2.8 A crystal structure of the aptamer bound to tetramethylrosamine (TMR), a high-affinity MG analog. The ligand-binding site is defined by an asymmetric internal loop, flanked by a pair of helices. A U-turn and several non-canonical base interactions stabilize the folding of loop nucleotides around the TMR. The aptamer utilizes several tiers of stacked nucleotides arranged in pairs, triples, and a novel base quadruple to effectively encapsulate the ligand. Even in the absence of specific stabilizing hydrogen bonds, discrimination between related fluorophores and chromophores is possible due to tight packing in the RNA binding pocket, which severely limits the size and shape of recognized ligands. The site of laser-induced cleavage lies relatively far from the bound TMR ( approximately 15 A). The unusual backbone conformation of the cleavage site nucleotide and its high level of solvent accessibility may combine to allow preferential reaction with freely diffusing hydroxyl radicals generated at the bound ligand. Several observations, however, favor alternative mechanisms for cleavage, such as conformational changes in the aptamer or long-range electron transfer between the bound ligand and the cleavage site nucleotide.
About this Structure
1F1T is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
2.8 A crystal structure of the malachite green aptamer., Baugh C, Grate D, Wilson C, J Mol Biol. 2000 Aug 4;301(1):117-28. PMID:10926496
Page seeded by OCA on Thu Feb 21 12:33:53 2008
Categories: Protein complex | Baugh, C. | Grate, D. | Wilson, C. | ROS | SR | 5-bromo-uridine | Base quadruple | Base triple | Gnra tetraloop | U-turn
