429d: Difference between revisions
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|PDB= 429d |SIZE=350|CAPTION= <scene name='initialview01'>429d</scene>, resolution 2.70Å | |PDB= 429d |SIZE=350|CAPTION= <scene name='initialview01'>429d</scene>, resolution 2.70Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | |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> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|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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[[Category: McKay, D. B.]] | [[Category: McKay, D. B.]] | ||
[[Category: Wedekind, J. E.]] | [[Category: Wedekind, J. E.]] | ||
[[Category: bulged nucleotide]] | [[Category: bulged nucleotide]] | ||
[[Category: lead-dependent cleavage]] | [[Category: lead-dependent cleavage]] | ||
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[[Category: trna internal loop]] | [[Category: trna internal loop]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:05 2008'' | ||
Revision as of 02:37, 31 March 2008
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| 429d, resolution 2.70Å | |||||||||||||
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| Ligands: | A, C, G, MG, U | ||||||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS
Overview
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.
About this Structure
429D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
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:10074945
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