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.


1yrm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:59, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yrm.gif|left|200px]]
 
-
{{Structure
+
==Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch==
-
|PDB= 1yrm |SIZE=350|CAPTION= <scene name='initialview01'>1yrm</scene>, resolution 2.50&Aring;
+
<StructureSection load='1yrm' size='340' side='right'caption='[[1yrm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=A5M:2&#39;-AMINE-CYTIDINE-5&#39;-MONOPHOSPHATE'>A5M</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+
<table><tr><td colspan='2'>[[1yrm]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YRM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YRM 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]] 2.5&#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=SR:STRONTIUM+ION'>SR</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yrm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yrm OCA], [https://pdbe.org/1yrm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yrm RCSB], [https://www.ebi.ac.uk/pdbsum/1yrm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yrm ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yrm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yrm OCA], [http://www.ebi.ac.uk/pdbsum/1yrm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yrm RCSB]</span>
+
__TOC__
-
}}
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
'''Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch'''
+
[[Category: Gherghe CM]]
-
 
+
[[Category: Krahn JM]]
-
 
+
[[Category: Weeks KM]]
-
==Overview==
+
-
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.
+
-
 
+
-
==About this Structure==
+
-
1YRM 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=1YRM 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: 2'-amine]]
+
-
[[Category: duplex]]
+
-
[[Category: mismatch]]
+
-
[[Category: rna]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:19:21 2008''
+

Current revision

Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch

PDB ID 1yrm

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/1yrm"
Personal tools