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.


1yn1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1yn1.gif|left|200px]]
+
{{Seed}}
 +
[[Image:1yn1.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_1yn1| PDB=1yn1 | SCENE= }}
{{STRUCTURE_1yn1| PDB=1yn1 | SCENE= }}
-
'''Solution structure of the VS ribozyme stem-loop V in the presence of MgCl2'''
+
===Solution structure of the VS ribozyme stem-loop V in the presence of MgCl2===
-
==Overview==
+
<!--
-
In the Neurospora VS ribozyme, magnesium ions facilitate formation of a loop-loop interaction between stem-loops I and V, which is important for recognition and activation of the stem-loop I substrate. Here, we present the high-resolution NMR structure of stem-loop V (SL5) in the presence of Mg(2+) (SL5(Mg)) and demonstrate that Mg(2+) induces a conformational change in which the SL5 loop adopts a compact structure with most characteristics of canonical U-turn structures. Divalent cation-binding sites were probed with Mn(2+)-induced paramagnetic line broadening and intermolecular NOEs to Co(NH(3))(6)(3+). Structural modeling of Mn(H(2)O)(6)(2+) in SL5(Mg) revealed four divalent cation-binding sites in the loop. Sites 1, 3, and 4 are located in the major groove near multiple phosphate groups, whereas site 2 is adjacent to N7 of G697 and N7 of A698 in the minor groove. Cation-binding sites equivalent to sites 1-3 in SL5 are present in other U-turn motifs, and these metal-binding sites may represent a common feature of the U-turn fold. Although magnesium ions affect the loop conformation, they do not significantly change the conformation of residues 697-699 involved in the proposed Watson-Crick base pairs with stem-loop I. In both the presence and the absence of Mg(2+), G697, A698, and C699 adopt an A-form structure that exposes their Watson-Crick faces, and this is compatible with their proposed interaction with stem-loop I. In SL5(Mg), however, U700 becomes exposed on the minor groove face of the loop in the proximity of the bases of G697, A698, and C699, suggesting that the Mg(2+)-bound conformation of stem-loop V allows additional contacts with stem-loop I. These studies improve our understanding of the role of Mg(2+) in U-turn structures and in substrate recognition by the VS ribozyme.
+
The line below this paragraph, {{ABSTRACT_PUBMED_16939211}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 16939211 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_16939211}}
==About this Structure==
==About this Structure==
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YN1 OCA].
+
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YN1 OCA].
==Reference==
==Reference==
Line 25: Line 29:
[[Category: Magnesium ion]]
[[Category: Magnesium ion]]
[[Category: U-turn]]
[[Category: U-turn]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:31:42 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 13:29:25 2008''

Revision as of 10:29, 27 July 2008

Image:1yn1.png

Template:STRUCTURE 1yn1

Solution structure of the VS ribozyme stem-loop V in the presence of MgCl2

Template:ABSTRACT PUBMED 16939211

About this Structure

Full experimental information is available from OCA.

Reference

NMR structure of varkud satellite ribozyme stem-loop V in the presence of magnesium ions and localization of metal-binding sites., Campbell DO, Bouchard P, Desjardins G, Legault P, Biochemistry. 2006 Sep 5;45(35):10591-605. PMID:16939211

Page seeded by OCA on Sun Jul 27 13:29:25 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yn1"
Personal tools