1r2p: Difference between revisions

Revision as of 15:46, 21 February 2008

Solution structure of domain 5 from the ai5(gamma) group II intron

OverviewOverview

Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.

About this StructureAbout this Structure

1R2P is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif., Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM, Nat Struct Mol Biol. 2004 Feb;11(2):187-92. Epub 2004 Jan 25. PMID:14745440

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-[[Image:1r2p.gif|left|200px]]<br /><applet load="1r2p" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1r2p" />
 '''Solution structure of domain 5 from the ai5(gamma) group II intron'''<br />
 ==Overview==
-Domain 5 (D5) is the central core of group II intron ribozymes. Many base, and backbone substituents of this highly conserved hairpin participate in, catalysis and are crucial for binding to other intron domains. We report, the solution structures of the 34-nucleotide D5 hairpin from the group II, intron ai5 gamma in the absence and presence of divalent metal ions. The, bulge region of D5 adopts a novel fold, where G26 adopts a syn, conformation and flips down into the major groove of helix 1, close to the, major groove face of the catalytic AGC triad. The backbone near G26 is, kinked, exposing the base plane of the adjacent A-U pair to the solvent, and causing bases of the bulge to stack intercalatively. Metal ion, titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5, bulge. Another distinct metal ion-binding site is observed along the minor, groove side of the catalytic triad, in a manner consistent with metal ion, binding in the ribozyme active site.
+Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.
 ==About this Structure==
-R2P is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R2P OCA].
+R2P is a [http://en.wikipedia.org/wiki/Protein_complex 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=1R2P OCA].
 ==Reference==
 Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif., Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM, Nat Struct Mol Biol. 2004 Feb;11(2):187-92. Epub 2004 Jan 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14745440 14745440]
 [[Category: Protein complex]]
-[[Category: Abramovitz, D.L.]]
+[[Category: Abramovitz, D L.]]
-[[Category: Butcher, S.E.]]
+[[Category: Butcher, S E.]]
-[[Category: III, A.G.Palmer.]]
+[[Category: III, A G.Palmer.]]
-[[Category: Pyle, A.M.]]
+[[Category: Pyle, A M.]]
-[[Category: Sashital, D.G.]]
+[[Category: Sashital, D G.]]
-[[Category: Sigel, R.K.O.]]
+[[Category: Sigel, R K.O.]]
 [[Category: bulge]]
 [[Category: magnesium]]
@@ Line 24: / Line 24: @@
 [[Category: tetraloop]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:59:52 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:46:23 2008''