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| [[Image:429d.gif|left|200px]]<br /><applet load="429d" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="429d, resolution 2.70Å" />
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| '''CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS'''<br />
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| ==Overview== | | ==CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS== |
| The leadzyme is a small RNA motif that catalyzes a site-specific, Pb2+-dependent cleavage reaction. As such, it is an example of a metal-dependent RNA enzyme. Here we describe the X-ray crystallographic structure of the leadzyme, which reveals two independent molecules per asymmetric unit. Both molecules feature an internal loop in which a bulged purine base stack twists away from the helical stem. This kinks the backbone, rendering the phosphodiester bond susceptible to cleavage. The independent molecules have different conformations: one leadzyme copy coordinates Mg2+, whereas the other binds only Ba2+ or Pb2+. In the active site of the latter molecule, a single Ba2+ ion coordinates the 2'-OH nucleophile, and appears to mimic the binding of catalytic lead. These observations allow a bond cleavage reaction to be modeled, which reveals the minimal structural features necessary for catalysis by this small ribozyme.
| | <StructureSection load='429d' size='340' side='right'caption='[[429d]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[429d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=429D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=429D FirstGlance]. <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]] 2.7Å</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></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=429d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=429d OCA], [https://pdbe.org/429d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=429d RCSB], [https://www.ebi.ac.uk/pdbsum/429d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=429d ProSAT]</span></td></tr> |
| | </table> |
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| ==About this Structure== | | ==See Also== |
| 429D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=429D OCA].
| | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
| | | __TOC__ |
| ==Reference==
| | </StructureSection> |
| Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis., Wedekind JE, McKay DB, Nat Struct Biol. 1999 Mar;6(3):261-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10074945 10074945]
| | [[Category: Large Structures]] |
| [[Category: Protein complex]] | | [[Category: McKay DB]] |
| [[Category: McKay, D. B.]] | | [[Category: Wedekind JE]] |
| [[Category: Wedekind, J. E.]] | |
| [[Category: MG]]
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| [[Category: bulged nucleotides]]
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| [[Category: lead-dependent cleavage]]
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| [[Category: leadzyme]]
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| [[Category: rna]]
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| [[Category: trna internal loop]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:12:08 2008''
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