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1nuv

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(New page: 200px<br /><applet load="1nuv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nuv, resolution 1.81&Aring;" /> '''The Leadzyme Ribozym...)
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[[Image:1nuv.gif|left|200px]]<br /><applet load="1nuv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nuv, resolution 1.81&Aring;" />
 
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'''The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution'''<br />
 
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==Overview==
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==The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution==
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The leadzyme is a small ribozyme, derived from in vitro selection, which, catalyzes site specific, Pb(2+)-dependent RNA cleavage. Pb(2+) is required, for activity; Mg(2+) inhibits activity, while many divalent and trivalent, ions enhance it. The leadzyme structure consists of an RNA duplex, interrupted by a trinucleotide bulge. Here, crystal structures determined, to 1.8 A resolution, both with Mg(2+) as the sole divalent counterion and, with Mg(2+) and Sr(2+) (which mimics Pb(2+) with respect to binding but, not catalysis), reveal the metal ion interactions with both the ground, state and precatalytic conformations of the leadzyme. Mg(H(2)O)(6)(2+), ions bridge complementary strands of the duplex at multiple locations by, binding tandem purines of one RNA strand in the major groove. At one site, Mg(H(2)O)(6)(2+) ligates the phosphodiester backbone of the trinucleotide, bulge in the ground state conformation, but not in the precatalytic, conformation, suggesting (a) Mg(2+) may inhibit leadzyme activity by, stabilizing the ground state and (b) metal ions which displace Mg(2+) from, this site may activate the leadzyme. Binding of Sr(2+) to the presumed, catalytic Pb(2+) site in the precatalytic leadzyme induces local, structural changes in a manner that would facilitate alignment of the, catalytic ribose 2'-hydroxyl with the scissile bond for cleavage. These, data support a model wherein binding of a catalytic ion to a precatalytic, conformation of the leadzyme, in conjunction with the flexibility of the, trinucleotide bulge, may facilitate structural rearrangements around the, scissle phosphodiester bond favoring configurations that allow bond, cleavage.
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<StructureSection load='1nuv' size='340' side='right'caption='[[1nuv]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1nuv]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NUV FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nuv OCA], [https://pdbe.org/1nuv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nuv RCSB], [https://www.ebi.ac.uk/pdbsum/1nuv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nuv ProSAT]</span></td></tr>
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</table>
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==About this Structure==
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==See Also==
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1NUV is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG and SR as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NUV OCA].
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation., Wedekind JE, McKay DB, Biochemistry. 2003 Aug 19;42(32):9554-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12911297 12911297]
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[[Category: Large Structures]]
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[[Category: Protein complex]]
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[[Category: Mckay DB]]
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[[Category: Mckay, D.B.]]
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[[Category: Wedekind JE]]
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[[Category: Wedekind, J.E.]]
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[[Category: MG]]
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[[Category: SR]]
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[[Category: alternate conformation]]
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[[Category: bulged nucleotides]]
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[[Category: homopurine base pairs]]
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[[Category: hydrated magnesium]]
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[[Category: lead-dependent cleavage]]
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[[Category: leadzyme]]
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[[Category: mg(h2o)6(ii)]]
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[[Category: pseudohelical packing]]
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[[Category: ribozyme]]
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[[Category: rna]]
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[[Category: sr(ii)]]
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[[Category: sticky ends]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:50:47 2007''
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Current revision

The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution

PDB ID 1nuv

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