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| [[Image:1yzd.gif|left|200px]]<br /><applet load="1yzd" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1yzd, resolution 2.35Å" />
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| '''Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair'''<br />
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| ==Overview== | | ==Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair== |
| 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.
| | <StructureSection load='1yzd' size='340' side='right'caption='[[1yzd]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1yzd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YZD FirstGlance]. <br> |
| 1YZD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YZD OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5M:2-AMINE-CYTIDINE-5-MONOPHOSPHATE'>A5M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| ==Reference==
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yzd OCA], [https://pdbe.org/1yzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yzd RCSB], [https://www.ebi.ac.uk/pdbsum/1yzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yzd ProSAT]</span></td></tr> |
| 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]
| | </table> |
| [[Category: Protein complex]]
| | __TOC__ |
| [[Category: Gherghe, C M.]]
| | </StructureSection> |
| [[Category: Krahn, J M.]]
| | [[Category: Large Structures]] |
| [[Category: Weeks, K M.]]
| | [[Category: Gherghe CM]] |
| [[Category: CA]] | | [[Category: Krahn JM]] |
| [[Category: 2'-amine]] | | [[Category: Weeks KM]] |
| [[Category: duplex]] | |
| [[Category: rna]] | |
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:10:38 2008''
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