2arg | pdb_00002arg

FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES

spinqualitylabelsall models 2arg, 9 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2arg is a 1 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ARM Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed BACKGROUND: In vitro selection has identified DNA aptamers that target cofactors, amino acids, peptides and proteins. Structure determination of such ligand-DNA aptamer complexes should elucidate the details of adaptive DNA structural transitions, binding-pocket architectures and ligand recognition. We have determined the solution structure of the complex of a DNA aptamer containing a guanine-rich 18-residue hairpin loop that binds L-argininamide with approximately 100 microM affinity. RESULTS: The DNA aptamer generates its L-argininamide-binding pocket by adaptive zippering up the 18-residue loop through formation of Watson-Crick pairs, mismatch pairs and base triples, while maximizing stacking interactions. Three of the four base triples involve minor-groove recognition through sheared G.A mismatch formation. The unique fold is also achieved through positioning of an adenine residue deep within the minor groove and through nestling of a smaller loop within the larger loop on complex formation. The accessibility to the unique L-argininamide-binding pocket is restricted by a base pair that bridges across one side of the major-groove-binding site. The guanidinium group of the bound L-argininamide aligns through intermolecular hydrogen-bond formation with the base edges of nonadjacent guanine and cytosine residues while being sandwiched between the planes of nonadjacent guanine residues. CONCLUSIONS: The available structures of L-arginine/L-argininamide bound to their DNA and RNA targets define the common principles and patterns associated with molecular recognition, as well as the diversity of intermolecular hydrogen-bonding alignments associated with the distinct binding pockets. Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop.,Lin CH, Wang W, Jones RA, Patel DJ Chem Biol. 1998 Oct;5(10):555-72. PMID:9818148 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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