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| - | [[Image:429d.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS== |
| - | |PDB= 429d |SIZE=350|CAPTION= <scene name='initialview01'>429d</scene>, resolution 2.70Å
| + | <StructureSection load='429d' size='340' side='right'caption='[[429d]], [[Resolution|resolution]] 2.70Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <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> |
| - | |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]] 2.7Å</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></td></tr> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=429d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=429d OCA], [http://www.ebi.ac.uk/pdbsum/429d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=429d RCSB]</span>
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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]] |
| - | 429D 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=429D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: McKay, D. B.]] | + | |
| - | [[Category: Wedekind, J. E.]] | + | |
| - | [[Category: bulged nucleotide]]
| + | |
| - | [[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 Mon Mar 31 05:37:05 2008''
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