1yy0: Difference between revisions

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<StructureSection load='1yy0' size='340' side='right'caption='[[1yy0]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
<StructureSection load='1yy0' size='340' side='right'caption='[[1yy0]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== 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 [http://oca.weizmann.ac.il/oca-docs/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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5M:2-AMINE-CYTIDINE-5-MONOPHOSPHATE'>A5M</scene>, <scene name='pdbligand=M5M:2-(N-ACETAMIDE)-CYTIDINE-5-MONOPHOSPHATE'>M5M</scene></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>, <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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yy0 OCA], [http://pdbe.org/1yy0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yy0 RCSB], [http://www.ebi.ac.uk/pdbsum/1yy0 PDBsum], [http://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>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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<ref>PMID:16190727</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1yy0" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Gherghe, C M]]
[[Category: Gherghe CM]]
[[Category: Krahn, J M]]
[[Category: Krahn JM]]
[[Category: Weeks, K M]]
[[Category: Weeks KM]]
[[Category: 2'-amine]]
[[Category: 2-amide]]
[[Category: Duplex]]
[[Category: In-crystal reaction]]
[[Category: Mismatch]]
[[Category: Rna]]

Latest revision as of 12:01, 14 February 2024

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

1yy0 is a 3 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1yy0, resolution 3.20Å

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