1z7f
From Proteopedia
(New page: 200px<br /><applet load="1z7f" size="450" color="white" frame="true" align="right" spinBox="true" caption="1z7f, resolution 2.10Å" /> '''Crystal structure of...) |
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| - | [[Image:1z7f.gif|left|200px]]<br /><applet load="1z7f" size=" | + | [[Image:1z7f.gif|left|200px]]<br /><applet load="1z7f" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1z7f, resolution 2.10Å" /> | caption="1z7f, resolution 2.10Å" /> | ||
'''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch'''<br /> | '''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Ribose 2'-amine substitutions are broadly useful as structural probes in | + | Ribose 2'-amine substitutions are broadly useful as structural probes in nucleic acids. In addition, structure-selective chemical reaction at 2'-amine groups is a robust technology for interrogating local nucleotide flexibility and conformational changes in RNA and DNA. We analyzed crystal structures for several RNA duplexes containing 2'-amino cytidine (C(N)) residues that form either C(N)-G base pairs or C(N)-A mismatches. The 2'-amine substitution is readily accommodated in an A-form RNA helix and thus differs from the C2'-endo conformation observed for free nucleosides. The 2'-amide product structure was visualized directly by acylating a C(N)-A mismatch in intact crystals and is also compatible with A-form geometry. To visualize conformations able to facilitate formation of the amide-forming transition state, in which the amine nucleophile carries a positive partial charge, we analyzed crystals of the C(N)-A duplex at pH 5, where the 2'-amine is protonated. The protonated amine moves to form a strong electrostatic interaction with the 3'-phosphodiester. Taken together with solution-phase experiments, 2'-amine acylation is likely facilitated by either of two transition states, both involving precise positioning of the adjacent 3'-phosphodiester group. |
==About this Structure== | ==About this Structure== | ||
| - | 1Z7F is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with SR as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1Z7F is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SR:'>SR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z7F OCA]. |
==Reference== | ==Reference== | ||
Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA., Gherghe CM, Krahn JM, Weeks KM, J Am Chem Soc. 2005 Oct 5;127(39):13622-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16190727 16190727] | Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA., Gherghe CM, Krahn JM, Weeks KM, J Am Chem Soc. 2005 Oct 5;127(39):13622-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16190727 16190727] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Gherghe, C | + | [[Category: Gherghe, C M.]] |
| - | [[Category: Krahn, J | + | [[Category: Krahn, J M.]] |
| - | [[Category: Weeks, K | + | [[Category: Weeks, K M.]] |
[[Category: SR]] | [[Category: SR]] | ||
[[Category: duplex]] | [[Category: duplex]] | ||
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[[Category: rna]] | [[Category: rna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:12:49 2008'' |
Revision as of 14:12, 21 February 2008
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Crystal structure of 16 base pair RNA duplex containing a C-A mismatch
Overview
Ribose 2'-amine substitutions are broadly useful as structural probes in nucleic acids. In addition, structure-selective chemical reaction at 2'-amine groups is a robust technology for interrogating local nucleotide flexibility and conformational changes in RNA and DNA. We analyzed crystal structures for several RNA duplexes containing 2'-amino cytidine (C(N)) residues that form either C(N)-G base pairs or C(N)-A mismatches. The 2'-amine substitution is readily accommodated in an A-form RNA helix and thus differs from the C2'-endo conformation observed for free nucleosides. The 2'-amide product structure was visualized directly by acylating a C(N)-A mismatch in intact crystals and is also compatible with A-form geometry. To visualize conformations able to facilitate formation of the amide-forming transition state, in which the amine nucleophile carries a positive partial charge, we analyzed crystals of the C(N)-A duplex at pH 5, where the 2'-amine is protonated. The protonated amine moves to form a strong electrostatic interaction with the 3'-phosphodiester. Taken together with solution-phase experiments, 2'-amine acylation is likely facilitated by either of two transition states, both involving precise positioning of the adjacent 3'-phosphodiester group.
About this Structure
1Z7F is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA., Gherghe CM, Krahn JM, Weeks KM, J Am Chem Soc. 2005 Oct 5;127(39):13622-8. PMID:16190727
Page seeded by OCA on Thu Feb 21 16:12:49 2008
Categories: Protein complex | Gherghe, C M. | Krahn, J M. | Weeks, K M. | SR | Duplex | Mismatch | Rna
