PDBsum entry 2gcs

RNA

PDB id: 2gcs

Contents

DNA/RNA

Metals

_MG ×6

Waters ×201

PDB id:

2gcs

Name:

RNA

Title:

Pre-cleavage state of the thermoanaerobacter tengcongensis glms ribozyme

Structure:

Glms ribozyme amino RNA inhibitor. Chain: a. Engineered: yes. Glms ribozyme RNA. Chain: b. Engineered: yes

Source:

Synthetic: yes. Other_details: this sequence occurs naturally in the thermoanaerobacter tengcongensis glms ribozyme. Other_details: in vitro transcription of sequnce from thermoanaerobacter tengcongensis

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.221 R-free: 0.245

Authors:

D.J.Klein,A.R.Ferre-D'Amare

Key ref:

D.J.Klein and A.R.Ferré-D'Amaré (2006). Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science, 313, 1752-1756. PubMed id: 16990543 DOI: 10.1126/science.1129666

Date:

14-Mar-06 Release date: 26-Sep-06

DNA/RNA chains

2AD-G-C-G-C-C-U-G-G-A-C-U-U-A-A-A-G-C-C-A-U 21 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-U-A-U-C-G-A-G-A-C-A-U-C-G- 123 bases

DOI no: 10.1126/science.1129666

Science 313:1752-1756 (2006)

PubMed id: 16990543

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.

D.J.Klein, A.R.Ferré-D'Amaré.

ABSTRACT

The glmS ribozyme is the only natural catalytic RNA known to require a small-molecule activator for catalysis. This catalytic RNA functions as a riboswitch, with activator-dependent RNA cleavage regulating glmS messenger RNA expression. We report crystal structures of the glmS ribozyme in precleavage states that are unliganded or bound to the competitive inhibitor glucose-6-phosphate and in the postcleavage state. All structures superimpose closely, revealing a remarkably rigid RNA that contains a preformed active and coenzyme-binding site. Unlike other riboswitches, the glmS ribozyme binds its activator in an open, solvent-accessible pocket. Our structures suggest that the amine group of the glmS ribozyme-bound coenzyme performs general acid-base and electrostatic catalysis.

Selected figure(s)

Figure 4.
Fig. 4. Coenzyme binding pocket. (A) Molecular surface of the glmS ribozyme (orientation corresponds to Fig. 1B). Nucleotides >90% conserved are colored green. Atomic spheres are shown for Glc6P and the Mg^2+ ion that coordinates its phosphate. (B) Expanded view of the Glc6P binding pocket. (C) Portion of the Glc6P-bound, 2'-deoxy A^(–1) precleavage structure superimposed on the residual simulated-annealing omit |F[o]| – |F[c]| electron density map contoured at 2.5 [orientation is rotated slightly from (A)] and a stick figure of the bound Glc6P. Hydrogen bonding interactions involving Glc6P and two active site water molecules (red spheres) are shown. The position of a modeled 2'-OH of A^(–1) is shown to indicate its proximity to one of the two buried waters.

Figure 5.
Fig. 5. GlcN6P-dependent cleavage of glmS ribozymes in the crystalline state. (A) Simulated-annealing omit |F[o]| – |F[c]| electron density (contoured at 3.0 ) calculated with data from an all-RNA crystal soaked in Glc6P and phases from a model lacking A^(–1), G^1, and Glc6P. (B) Simulated-annealing omit |F[o]| – |F[c]| electron density (contoured at 3.0 ) calculated with data from an all-RNA crystal soaked in GlcN6P and phases from a model lacking A^(–1), G^1, and Glc6P.

The above figures are reprinted by permission from the AAAs: Science (2006, 313, 1752-1756) copyright 2006.

Figures were selected by the author.