1kod
From Proteopedia
(New page: 200px<br /><applet load="1kod" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kod" /> '''RNA APTAMER COMPLEXED WITH CITRULLINE, NMR''...) |
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| - | [[Image:1kod.jpg|left|200px]]<br /><applet load="1kod" size=" | + | [[Image:1kod.jpg|left|200px]]<br /><applet load="1kod" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1kod" /> | caption="1kod" /> | ||
'''RNA APTAMER COMPLEXED WITH CITRULLINE, NMR'''<br /> | '''RNA APTAMER COMPLEXED WITH CITRULLINE, NMR'''<br /> | ||
==Overview== | ==Overview== | ||
| - | In a previous study, an RNA aptamer for the specific recognition of | + | In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket. |
==About this Structure== | ==About this Structure== | ||
| - | 1KOD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CIR as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1KOD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CIR:'>CIR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KOD OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Kochoyan, M.]] | [[Category: Kochoyan, M.]] | ||
[[Category: Westhof, E.]] | [[Category: Westhof, E.]] | ||
| - | [[Category: Yang, Y | + | [[Category: Yang, Y S.]] |
[[Category: CIR]] | [[Category: CIR]] | ||
[[Category: in vitro selected rna]] | [[Category: in vitro selected rna]] | ||
[[Category: rna aptamer]] | [[Category: rna aptamer]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:36:16 2008'' |
Revision as of 11:36, 21 February 2008
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RNA APTAMER COMPLEXED WITH CITRULLINE, NMR
Overview
In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.
About this Structure
1KOD is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy., Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M, Science. 1996 May 31;272(5266):1343-7. PMID:8650546
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