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| - | [[Image:1nuv.gif|left|200px]] | |
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| - | {{Structure
| + | ==The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution== |
| - | |PDB= 1nuv |SIZE=350|CAPTION= <scene name='initialview01'>1nuv</scene>, resolution 1.81Å
| + | <StructureSection load='1nuv' size='340' side='right'caption='[[1nuv]], [[Resolution|resolution]] 1.81Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=SR:STRONTIUM ION'>SR</scene> | + | <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> |
| - | |ACTIVITY=
| + | </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> |
| - | |GENE=
| + | <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 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> |
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| - | '''The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution'''
| + | ==See Also== |
| - | | + | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview==
| + | </StructureSection> |
| - | 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.
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Mckay DB]] |
| - | ==About this Structure== | + | [[Category: Wedekind JE]] |
| - | 1NUV is a [[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=1NUV OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/12911297 12911297]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Mckay, D B.]] | + | |
| - | [[Category: Wedekind, J E.]] | + | |
| - | [[Category: MG]]
| + | |
| - | [[Category: SR]]
| + | |
| - | [[Category: alternate conformation]]
| + | |
| - | [[Category: bulged nucleotide]]
| + | |
| - | [[Category: homopurine base pair]]
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| - | [[Category: hydrated magnesium]]
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| - | [[Category: lead-dependent cleavage]]
| + | |
| - | [[Category: leadzyme]]
| + | |
| - | [[Category: mg(h2o)6(ii)]]
| + | |
| - | [[Category: pseudohelical packing]]
| + | |
| - | [[Category: ribozyme]]
| + | |
| - | [[Category: rna]]
| + | |
| - | [[Category: sr(ii)]]
| + | |
| - | [[Category: sticky end]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:02:01 2008''
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