1yy0: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1yy0]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YY0 FirstGlance]. <br> | <table><tr><td colspan='2'>[[1yy0]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YY0 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2Å</td></tr> | ||
<tr id=' | <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>, <scene name='pdbligand=M5M:2-(N-ACETAMIDE)-CYTIDINE-5-MONOPHOSPHATE'>M5M</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yy0 OCA], [https://pdbe.org/1yy0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yy0 RCSB], [https://www.ebi.ac.uk/pdbsum/1yy0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yy0 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yy0 OCA], [https://pdbe.org/1yy0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yy0 RCSB], [https://www.ebi.ac.uk/pdbsum/1yy0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yy0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Gherghe | [[Category: Gherghe CM]] | ||
[[Category: Krahn | [[Category: Krahn JM]] | ||
[[Category: Weeks | [[Category: Weeks KM]] | ||
Revision as of 10:15, 9 August 2023
Crystal structure of an RNA duplex containing a 2'-amine substitution and a 2'-amide product produced by in-crystal acylation at a C-A mismatchCrystal structure of an RNA duplex containing a 2'-amine substitution and a 2'-amide product produced by in-crystal acylation at a C-A mismatch
Structural highlights
Publication Abstract from PubMedRibose 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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