1yn2: Difference between revisions

Revision as of 17:07, 21 February 2008

Solution structure of the Neurospora VS ribozyme stem-loop V in the presence of MgCl2 with modeling of bound manganese ions

OverviewOverview

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.

About this StructureAbout this Structure

1YN2 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

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 Thu Feb 21 16:07:10 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1yn2.gif|left|200px]]<br /><applet load="1yn2" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1yn2.gif|left|200px]]<br /><applet load="1yn2" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1yn2" />
 '''Solution structure of the Neurospora VS ribozyme stem-loop V in the presence of MgCl2 with modeling of bound manganese ions'''<br />
 ==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.
+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.
 ==About this Structure==
-YN2 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YN2 OCA].
+YN2 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YN2 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16939211 16939211]
 [[Category: Protein complex]]
-[[Category: Campbell, D.O.]]
+[[Category: Campbell, D O.]]
 [[Category: Legault, P.]]
 [[Category: MN]]
 [[Category: u-turn; hairpin; magnesium ions; manganese ions; paramagnetic]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:23:01 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:07:10 2008''