1NUV

The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution

Summary for 1NUV

• Entry DOI: 10.2210/pdb1nuv/pdb
• Related: 1LDZ 1NUJ 2LDZ 429D
• Descriptor: 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3', 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3', MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: ribozyme, leadzyme, lead-dependent cleavage, rna, mg(h2o)6(ii), bulged nucleotides, hydrated magnesium, sr(ii), pseudohelical packing, sticky ends, alternate conformation, homopurine base pairs
• Total number of polymer chains: 8
• Total formula weight: 31699.78

Authors

Wedekind, J.E.,Mckay, D.B. (deposition date: 2003-02-01, release date: 2003-08-19, Last modification date: 2024-04-03)

Primary citation

Wedekind, J.E.,McKay, D.B.
Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation.
BIOCHEMISTRY, 42:9554-9563, 2003

PubMed Abstract: The leadzyme is a small ribozyme, derived from in vitro selection, which catalyzes site specific, Pb(2+)-dependent RNA cleavage. Pb(2+) is required for activity; Mg(2+) inhibits activity, while many divalent and trivalent ions enhance it. The leadzyme structure consists of an RNA duplex interrupted by a trinucleotide bulge. Here, crystal structures determined to 1.8 A resolution, both with Mg(2+) as the sole divalent counterion and with Mg(2+) and Sr(2+) (which mimics Pb(2+) with respect to binding but not catalysis), reveal the metal ion interactions with both the ground state and precatalytic conformations of the leadzyme. Mg(H(2)O)(6)(2+) ions bridge complementary strands of the duplex at multiple locations by binding tandem purines of one RNA strand in the major groove. At one site, Mg(H(2)O)(6)(2+) ligates the phosphodiester backbone of the trinucleotide bulge in the ground state conformation, but not in the precatalytic conformation, suggesting (a) Mg(2+) may inhibit leadzyme activity by stabilizing the ground state and (b) metal ions which displace Mg(2+) from this site may activate the leadzyme. Binding of Sr(2+) to the presumed catalytic Pb(2+) site in the precatalytic leadzyme induces local structural changes in a manner that would facilitate alignment of the catalytic ribose 2'-hydroxyl with the scissile bond for cleavage. These data support a model wherein binding of a catalytic ion to a precatalytic conformation of the leadzyme, in conjunction with the flexibility of the trinucleotide bulge, may facilitate structural rearrangements around the scissle phosphodiester bond favoring configurations that allow bond cleavage.

PubMed: 12911297
DOI: 10.1021/bi0300783

Experimental method

X-RAY DIFFRACTION (1.81 Å)