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2arg

From Proteopedia

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[[Image:2arg.jpg|left|200px]]
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[[Image:2arg.png|left|200px]]
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{{STRUCTURE_2arg| PDB=2arg | SCENE= }}
{{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'''
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===FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 9818148 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9818148}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARG OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARG OCA].
==Reference==
==Reference==
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[[Category: Minor groove recognition]]
[[Category: Minor groove recognition]]
[[Category: Molecular recognition of an amino acid]]
[[Category: Molecular recognition of an amino acid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:23:08 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 16:20:19 2008''

Revision as of 13:20, 27 July 2008

Image:2arg.png

Template:STRUCTURE 2arg

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

Template:ABSTRACT PUBMED 9818148

About this Structure

Full experimental 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 Sun Jul 27 16:20:19 2008

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