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| | ==The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution== | | ==The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution== |
| - | <StructureSection load='1nuv' size='340' side='right' caption='[[1nuv]], [[Resolution|resolution]] 1.81Å' scene=''> | + | <StructureSection load='1nuv' size='340' side='right'caption='[[1nuv]], [[Resolution|resolution]] 1.81Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NUV FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[429d|429d]], [[1ldz|1ldz]], [[2ldz|2ldz]], [[1nuj|1nuj]]</td></tr> | + | <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> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nuv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nuv RCSB], [http://www.ebi.ac.uk/pdbsum/1nuv PDBsum]</span></td></tr> | + | <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> |
| - | <table> | + | </table> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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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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| - | 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:12911297<ref>PMID:12911297</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| | ==See Also== | | ==See Also== |
| - | *[[Ribozyme|Ribozyme]] | + | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Mckay, D B.]] | + | [[Category: Large Structures]] |
| - | [[Category: Wedekind, J E.]] | + | [[Category: Mckay DB]] |
| - | [[Category: Alternate conformation]] | + | [[Category: Wedekind JE]] |
| - | [[Category: Bulged nucleotide]]
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| - | [[Category: Homopurine base pair]]
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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: Pseudohelical packing]]
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| - | [[Category: Ribozyme]]
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| - | [[Category: Rna]]
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| - | [[Category: Sticky end]]
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