2arg: Difference between revisions

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{{Seed}}
[[Image:2arg.png|left|200px]]


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==FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES==
The line below this paragraph, containing "STRUCTURE_2arg", creates the "Structure Box" on the page.
<StructureSection load='2arg' size='340' side='right'caption='[[2arg]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2arg]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ARG FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene></td></tr>
{{STRUCTURE_2arg|  PDB=2arg  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2arg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2arg OCA], [https://pdbe.org/2arg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2arg RCSB], [https://www.ebi.ac.uk/pdbsum/2arg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2arg ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== 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, NMR, 9 STRUCTURES===
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<ref>PMID:9818148</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_9818148}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2arg" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 9818148 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_9818148}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARG OCA].
[[Category: Jones RA]]
 
[[Category: Lin CH]]
==Reference==
[[Category: Patel DJ]]
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: Wang W]]
[[Category: Jones, R A.]]
[[Category: Lin, C H.]]
[[Category: Patel, D J.]]
[[Category: Wang, W.]]
[[Category: Adaptive dna structural transition]]
[[Category: Base encapsulation within minor groove]]
[[Category: Deoxyribonucleic acid]]
[[Category: Dna aptamer]]
[[Category: L-argininamide binding pocket]]
[[Category: Minor groove recognition]]
[[Category: Molecular recognition of an amino acid]]
 
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