1ddy
From Proteopedia
(New page: 200px<br /> <applet load="1ddy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ddy, resolution 3.0Å" /> '''MOLECULAR RECOGNITIO...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1ddy.gif|left|200px]]<br /> | + | [[Image:1ddy.gif|left|200px]]<br /><applet load="1ddy" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="1ddy" size=" | + | |
caption="1ddy, resolution 3.0Å" /> | caption="1ddy, resolution 3.0Å" /> | ||
'''MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER'''<br /> | '''MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Previous solution structures of ligand-binding RNA aptamers have shown | + | Previous solution structures of ligand-binding RNA aptamers have shown that molecular recognition is achieved by the folding of an initially unstructured RNA around its cognate ligand, coupling the processes of RNA folding and binding. The 3 A crystal structure of the cyanocobalamin (vitamin B12) aptamer reported here suggests a different approach to molecular recognition in which elements of RNA secondary structure combine to create a solvent-accessible docking surface for a large, complex ligand. Central to this structure is a locally folding RNA triplex, stabilized by a novel three-stranded zipper. Perpendicular stacking of a duplex on this triplex creates a cleft that functions as the vitamin B12 binding site. Complementary packing of hydrophobic surfaces, direct hydrogen bonding and dipolar interactions between the ligand and the RNA appear to contribute to binding. The nature of the interactions that stabilize complex formation and the possible uncoupling of folding and binding for this RNA suggest a strong mechanistic similarity to typical protein-ligand complexes. |
==About this Structure== | ==About this Structure== | ||
| - | 1DDY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with B12 and NME as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1DDY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=B12:'>B12</scene> and <scene name='pdbligand=NME:'>NME</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DDY OCA]. |
==Reference== | ==Reference== | ||
The structural basis for molecular recognition by the vitamin B 12 RNA aptamer., Sussman D, Nix JC, Wilson C, Nat Struct Biol. 2000 Jan;7(1):53-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10625428 10625428] | The structural basis for molecular recognition by the vitamin B 12 RNA aptamer., Sussman D, Nix JC, Wilson C, Nat Struct Biol. 2000 Jan;7(1):53-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10625428 10625428] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Nix, J | + | [[Category: Nix, J C.]] |
[[Category: Sussman, D.]] | [[Category: Sussman, D.]] | ||
[[Category: Wilson, C.]] | [[Category: Wilson, C.]] | ||
| Line 23: | Line 22: | ||
[[Category: vitamin b12]] | [[Category: vitamin b12]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:41 2008'' |
Revision as of 10:15, 21 February 2008
|
MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER
Overview
Previous solution structures of ligand-binding RNA aptamers have shown that molecular recognition is achieved by the folding of an initially unstructured RNA around its cognate ligand, coupling the processes of RNA folding and binding. The 3 A crystal structure of the cyanocobalamin (vitamin B12) aptamer reported here suggests a different approach to molecular recognition in which elements of RNA secondary structure combine to create a solvent-accessible docking surface for a large, complex ligand. Central to this structure is a locally folding RNA triplex, stabilized by a novel three-stranded zipper. Perpendicular stacking of a duplex on this triplex creates a cleft that functions as the vitamin B12 binding site. Complementary packing of hydrophobic surfaces, direct hydrogen bonding and dipolar interactions between the ligand and the RNA appear to contribute to binding. The nature of the interactions that stabilize complex formation and the possible uncoupling of folding and binding for this RNA suggest a strong mechanistic similarity to typical protein-ligand complexes.
About this Structure
1DDY is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
The structural basis for molecular recognition by the vitamin B 12 RNA aptamer., Sussman D, Nix JC, Wilson C, Nat Struct Biol. 2000 Jan;7(1):53-7. PMID:10625428
Page seeded by OCA on Thu Feb 21 12:15:41 2008
Categories: Protein complex | Nix, J C. | Sussman, D. | Wilson, C. | B12 | NME | Aptamer | Rna | Triplex | Vitamin b12
