From Proteopedia
(Difference between revisions)
proteopedia linkproteopedia link
|
|
| Line 1: |
Line 1: |
| - | [[Image:2arg.jpg|left|200px]] | + | {{Seed}} |
| | + | [[Image:2arg.png|left|200px]] |
| | | | |
| | <!-- | | <!-- |
| Line 9: |
Line 10: |
| | {{STRUCTURE_2arg| PDB=2arg | SCENE= }} | | {{STRUCTURE_2arg| PDB=2arg | SCENE= }} |
| | | | |
| - | '''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=== |
| | | | |
| | | | |
| - | ==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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_9818148}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 9818148 is the PubMed ID number. |
| | + | --> |
| | + | {{ABSTRACT_PUBMED_9818148}} |
| | | | |
| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARG OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARG OCA]. |
| | | | |
| | ==Reference== | | ==Reference== |
| Line 31: |
Line 35: |
| | [[Category: Minor groove recognition]] | | [[Category: Minor groove recognition]] |
| | [[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 Sat May 3 19:23:08 2008'' | + | |
| | + | ''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
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
