2arg
From Proteopedia
(New page: 200px<br /><applet load="2arg" size="350" color="white" frame="true" align="right" spinBox="true" caption="2arg" /> '''FORMATION OF AN AMINO ACID BINDING POCKET TH...) |
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==Overview== | ==Overview== | ||
| - | BACKGROUND: In vitro selection has identified DNA aptamers that target | + | 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== | ==About this Structure== | ||
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=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://ispc.weizmann.ac.il//pmbin/getpm?pmid=9818148 9818148] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Jones, R | + | [[Category: Jones, R A.]] |
| - | [[Category: Lin, C | + | [[Category: Lin, C H.]] |
| - | [[Category: Patel, D | + | [[Category: Patel, D J.]] |
[[Category: Wang, W.]] | [[Category: Wang, W.]] | ||
[[Category: ARM]] | [[Category: ARM]] | ||
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[[Category: molecular recognition of an amino acid]] | [[Category: molecular recognition of an amino acid]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:30:13 2008'' |
Revision as of 14:30, 21 February 2008
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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
2ARG is a Protein complex structure of sequences from [1] with as ligand. 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 Thu Feb 21 16:30:13 2008
Categories: Protein complex | Jones, R A. | Lin, C H. | Patel, D J. | Wang, W. | ARM | Adaptive dna structural transitions | Base encapsulation within minor groove | Deoxyribonucleic acid | Dna aptamer | L-argininamide binding pocket | Minor groove recognition | Molecular recognition of an amino acid
