429d: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:429d.gif|left|200px]] | [[Image:429d.gif|left|200px]] | ||
'''CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS''' | {{Structure | ||
|PDB= 429d |SIZE=350|CAPTION= <scene name='initialview01'>429d</scene>, resolution 2.70Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
429D is a [ | 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]. | ||
==Reference== | ==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:// | 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: Protein complex]] | ||
[[Category: McKay, D. B.]] | [[Category: McKay, D. B.]] | ||
[[Category: Wedekind, J. E.]] | [[Category: Wedekind, J. E.]] | ||
[[Category: MG]] | [[Category: MG]] | ||
[[Category: bulged | [[Category: bulged nucleotide]] | ||
[[Category: lead-dependent cleavage]] | [[Category: lead-dependent cleavage]] | ||
[[Category: leadzyme]] | [[Category: leadzyme]] | ||
| Line 21: | Line 30: | ||
[[Category: trna internal loop]] | [[Category: trna internal loop]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:08:10 2008'' | ||
Revision as of 17:08, 20 March 2008
| |||||||||||||
| 429d, resolution 2.70Å | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ligands: | MG | ||||||||||||
| 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
Page seeded by OCA on Thu Mar 20 19:08:10 2008
