This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1yy0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:01, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yy0.gif|left|200px]]
 
-
{{Structure
+
==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 mismatch==
-
|PDB= 1yy0 |SIZE=350|CAPTION= <scene name='initialview01'>1yy0</scene>, resolution 3.20&Aring;
+
<StructureSection load='1yy0' size='340' side='right'caption='[[1yy0]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
+
<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>
-
|ACTIVITY=
+
</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>
-
|GENE=
+
<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>
-
 
+
</table>
-
'''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 mismatch'''
+
__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==
+
-
1YY0 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YY0 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]
+
-
[[Category: Protein complex]]
+
-
[[Category: Gherghe, C M.]]
+
-
[[Category: Krahn, J M.]]
+
-
[[Category: Weeks, K M.]]
+
-
[[Category: CA]]
+
-
[[Category: 2'-amine]]
+
-
[[Category: 2-amide]]
+
-
[[Category: duplex]]
+
-
[[Category: in-crystal reaction]]
+
-
[[Category: mismatch]]
+
-
[[Category: rna]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:28:53 2008''
+

Current revision

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 mismatch

PDB ID 1yy0

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yy0"
Personal tools