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
Line 1: Line 1:
-
[[Image:1yrm.gif|left|200px]]<br /><applet load="1yrm" size="350" color="white" frame="true" align="right" spinBox="true"
+
[[Image:1yrm.gif|left|200px]]
-
caption="1yrm, resolution 2.50&Aring;" />
+
 
-
'''Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch'''<br />
+
{{Structure
 +
|PDB= 1yrm |SIZE=350|CAPTION= <scene name='initialview01'>1yrm</scene>, resolution 2.50&Aring;
 +
|SITE=
 +
|LIGAND= <scene name='pdbligand=SR:STRONTIUM ION'>SR</scene>
 +
|ACTIVITY=
 +
|GENE=
 +
}}
 +
 
 +
'''Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a C-A mismatch'''
 +
 
==Overview==
==Overview==
Line 7: Line 16:
==About this Structure==
==About this Structure==
-
1YRM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SR:'>SR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YRM OCA].
+
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==
==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://ispc.weizmann.ac.il//pmbin/getpm?pmid=16190727 16190727]
+
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: Protein complex]]
[[Category: Gherghe, C M.]]
[[Category: Gherghe, C M.]]
Line 21: Line 30:
[[Category: rna]]
[[Category: rna]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:08:21 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:26:36 2008''

Revision as of 13:26, 20 March 2008

Image:1yrm.gif


PDB ID 1yrm

Drag the structure with the mouse to rotate
, resolution 2.50Å
Ligands:
Coordinates: save as pdb, mmCIF, xml



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


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 [1]. Full crystallographic information is available from 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:16190727

Page seeded by OCA on Thu Mar 20 15:26:36 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

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