429D

CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS

Summary for 429D

• Entry DOI: 10.2210/pdb429d/pdb
• Descriptor: RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'), RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: leadzyme, lead-dependent cleavage, trna internal loop, rna, bulged nucleotides
• Total number of polymer chains: 4
• Total formula weight: 15514.11

Authors

Wedekind, J.E.,McKay, D.B. (deposition date: 1998-09-29, release date: 1999-03-01, Last modification date: 2024-02-28)

Primary citation

Wedekind, J.E.,McKay, D.B.
Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis.
Nat.Struct.Biol., 6:261-268, 1999

PubMed Abstract: 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.

PubMed: 10074945
DOI: 10.1038/6700

Experimental method

X-RAY DIFFRACTION (2.7 Å)