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| <!-- | | ==CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS== |
| The line below this paragraph, containing "STRUCTURE_429d", creates the "Structure Box" on the page.
| | <StructureSection load='429d' size='340' side='right'caption='[[429d]], [[Resolution|resolution]] 2.70Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <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> |
| or leave the SCENE parameter empty for the default display.
| | </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> |
| {{STRUCTURE_429d| PDB=429d | SCENE= }}
| | <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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| '''CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS'''
| | ==See Also== |
| | | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
| | | __TOC__ |
| ==Overview==
| | </StructureSection> |
| 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.
| | [[Category: Large Structures]] |
| | | [[Category: McKay DB]] |
| ==About this Structure== | | [[Category: Wedekind JE]] |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=429D OCA].
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| ==Reference==
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| 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://www.ncbi.nlm.nih.gov/pubmed/10074945 10074945]
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| [[Category: McKay, D. B.]]
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| [[Category: Wedekind, J. E.]]
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| [[Category: Bulged nucleotide]]
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| [[Category: Lead-dependent cleavage]] | |
| [[Category: Leadzyme]] | |
| [[Category: Rna]] | |
| [[Category: Trna internal loop]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:17:21 2008''
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