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| [[Image:1yzd.gif|left|200px]]
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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== |
| The line below this paragraph, containing "STRUCTURE_1yzd", creates the "Structure Box" on the page.
| | <StructureSection load='1yzd' size='340' side='right'caption='[[1yzd]], [[Resolution|resolution]] 2.35Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <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> |
| or leave the SCENE parameter empty for the default display.
| | </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> |
| {{STRUCTURE_1yzd| PDB=1yzd | SCENE= }}
| | <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> |
| | | </table> |
| '''Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair'''
| | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Gherghe CM]] |
| 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.
| | [[Category: Krahn JM]] |
| | | [[Category: Weeks KM]] |
| ==About this Structure== | |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YZD 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:[http://www.ncbi.nlm.nih.gov/pubmed/16190727 16190727]
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| [[Category: Gherghe, C M.]] | |
| [[Category: Krahn, J M.]]
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| [[Category: Weeks, K M.]] | |
| [[Category: 2'-amine]] | |
| [[Category: Duplex]] | |
| [[Category: Rna]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:59:49 2008''
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