PDBsum entry 4meh

RNA

PDB id: 4meh

Contents

DNA/RNA

Metals

_CA ×9

Waters ×2

PDB id:

4meh

Name:

RNA

Title:

In vitro evolved glms ribozyme triple mutant, calcium ion complex

Structure:

Glms triple mutant ribozyme. Chain: a. Engineered: yes. (122-mer) ribozyme. Chain: b. Engineered: yes

Source:

Synthetic: yes. Other_details: this mutant ribozyme was evolved from the thermoanaerobacter tengcongensis glms ribozyme. Synthetic: yes

Resolution:

3.12Å R-factor: 0.231 R-free: 0.273

Authors:

M.W.L.Lau,A.R.Ferre-D'Amare

Key ref:

M.W.Lau and A.R.Ferré-D'Amaré (2013). An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol, 9, 805-810. PubMed id: 24096303 DOI: 10.1038/nchembio.1360

Date:

26-Aug-13 Release date: 16-Oct-13

DNA/RNA chains

A-G-C-G-C-C-U-G-G-A-C-U-U-A-A-A-G-C-C-A-U-U 22 bases

G-G-C-U-U-U-A-A-G-U-U-G-A-C-G-A-G-G-G-C-A-G-G-G-U-U-A-A-A-C-G-A-G-A-C-A-U-C-G- 122 bases

DOI no: 10.1038/nchembio.1360

Nat Chem Biol 9:805-810 (2013)

PubMed id: 24096303

An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence.

M.W.Lau, A.R.Ferré-D'Amaré.

ABSTRACT

Uniquely among known ribozymes, the glmS ribozyme-riboswitch requires a small-molecule coenzyme, glucosamine-6-phosphate (GlcN6P). Although consistent with its gene-regulatory function, the use of GlcN6P is unexpected because all of the other characterized self-cleaving ribozymes use RNA functional groups or divalent cations for catalysis. To determine what active site features make this ribozyme reliant on GlcN6P and to evaluate whether it might have evolved from a coenzyme-independent ancestor, we isolated a GlcN6P-independent variant through in vitro selection. Three active site mutations suffice to generate a highly reactive RNA that adopts the wild-type fold but uses divalent cations for catalysis and is insensitive to GlcN6P. Biochemical and crystallographic comparisons of wild-type and mutant ribozymes show that a handful of functional groups fine-tune the RNA to be either coenzyme or cation dependent. These results indicate that a few mutations can confer new biochemical activities on structured RNAs. Thus, families of structurally related ribozymes with divergent function may exist.