1NUJ

THE LEADZYME STRUCTURE BOUND TO MG(H20)6(II) AT 1.8 A RESOLUTION

1NUJ の概要

• エントリーDOI: 10.2210/pdb1nuj/pdb
• 関連するPDBエントリー: 1LDZ 1NUV 2LDZ 429D
• 分子名称: 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, ... (4 entities in total)
• 機能のキーワード: ribozyme, leadzyme, lead-dependent cleavage, rna, mg(h20)62+, bulged nucleotides, hydrated magnesium, pseudohelical packing, sticky ends, alternate conformation, homopurine base pairs
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 31174.06

構造登録者

Wedekind, J.E.,Mckay, D.B. (登録日: 2003-01-31, 公開日: 2003-08-19, 最終更新日: 2024-04-03)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.8 Å)