2arg: Difference between revisions
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[[Image:2arg.jpg|left|200px]] | [[Image:2arg.jpg|left|200px]] | ||
'''FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES''' | {{Structure | ||
|PDB= 2arg |SIZE=350|CAPTION= <scene name='initialview01'>2arg</scene> | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=ARM:DEOXY-METHYL-ARGININE'>ARM</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2ARG is a [ | 2ARG is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. 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:// | 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: Protein complex]] | ||
[[Category: Jones, R A.]] | [[Category: Jones, R A.]] | ||
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[[Category: Wang, W.]] | [[Category: Wang, W.]] | ||
[[Category: ARM]] | [[Category: ARM]] | ||
[[Category: adaptive dna structural | [[Category: adaptive dna structural transition]] | ||
[[Category: base encapsulation within minor groove]] | [[Category: base encapsulation within minor groove]] | ||
[[Category: deoxyribonucleic acid]] | [[Category: deoxyribonucleic acid]] | ||
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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 Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:52:59 2008'' | ||
Revision as of 13:53, 20 March 2008
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| Ligands: | ARM | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
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]. 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
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