1F1T
CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE
Summary for 1F1T
| Entry DOI | 10.2210/pdb1f1t/pdb |
| Descriptor | MALACHITE GREEN APTAMER RNA, STRONTIUM ION, N,N'-TETRAMETHYL-ROSAMINE, ... (4 entities in total) |
| Functional Keywords | u-turn, base quadruple, base triple, gnra tetraloop, 5-bromo-uridine, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 13756.30 |
| Authors | Baugh, C.,Grate, D.,Wilson, C. (deposition date: 2000-05-19, release date: 2000-09-04, Last modification date: 2024-02-07) |
| Primary citation | Baugh, C.,Grate, D.,Wilson, C. 2.8 A crystal structure of the malachite green aptamer. J.Mol.Biol., 301:117-128, 2000 Cited by PubMed Abstract: 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. PubMed: 10926496DOI: 10.1006/jmbi.2000.3951 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
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