2NPY

Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1

Summary for 2NPY

• Entry DOI: 10.2210/pdb2npy/pdb
• Related: 1ZFR 2NPZ
• Descriptor: 5'-R(*UP*CP*CP*CP*(U2N)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', ... (7 entities in total)
• Functional Keywords: hairpin ribozyme, mutation, s-turn, e-loop, ribose zipper, catalytic rna, 2'-deoxy 2'-amino, 9s linker, rna
• Total number of polymer chains: 4
• Total formula weight: 19917.18

Authors

MacElrevey, C.,Krucinska, J.,Wedekind, J.E. (deposition date: 2006-10-30, release date: 2007-08-14, Last modification date: 2023-08-30)

Primary citation

MacElrevey, C.,Spitale, R.C.,Krucinska, J.,Wedekind, J.E.
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
Acta Crystallogr.,Sect.D, 63:812-825, 2007

PubMed Abstract: The hairpin ribozyme is a small catalytic RNA comprising two helix-loop-helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5'-U to form an intermolecular U.U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 A resolution or better. In contrast, C3L variants diffracted to 3.35 A and exhibited a 15 A expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6(1) contacts, which comprise numerous backbone to 2'-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.

PubMed: 17582172
DOI: 10.1107/S090744490702464X

Experimental method

X-RAY DIFFRACTION (2.65 Å)