2arg
From Proteopedia
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[[Image:2arg.jpg|left|200px]] | [[Image:2arg.jpg|left|200px]] | ||
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| - | + | {{STRUCTURE_2arg| PDB=2arg | SCENE= }} | |
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'''FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES''' | '''FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARG OCA]. | |
==Reference== | ==Reference== | ||
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:[http://www.ncbi.nlm.nih.gov/pubmed/9818148 9818148] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/9818148 9818148] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Jones, R A.]] | [[Category: Jones, R A.]] | ||
[[Category: Lin, C H.]] | [[Category: Lin, C H.]] | ||
[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
[[Category: Wang, W.]] | [[Category: Wang, W.]] | ||
| - | [[Category: | + | [[Category: Adaptive dna structural transition]] |
| - | [[Category: | + | [[Category: Base encapsulation within minor groove]] |
| - | [[Category: | + | [[Category: Deoxyribonucleic acid]] |
| - | [[Category: | + | [[Category: Dna aptamer]] |
| - | [[Category: | + | [[Category: L-argininamide binding pocket]] |
| - | [[Category: | + | [[Category: Minor groove recognition]] |
| - | [[Category: | + | [[Category: Molecular recognition of an amino acid]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:23:08 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 16:23, 3 May 2008
FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES
Overview
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.
About this Structure
Full crystallographic information is available from OCA.
Reference
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 Page seeded by OCA on Sat May 3 19:23:08 2008
