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PDBsum entry 2h0x
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References listed in PDB file
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Key reference
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Title
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Structural basis of glms ribozyme activation by glucosamine-6-Phosphate.
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Authors
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D.J.Klein,
A.R.Ferré-D'Amaré.
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Ref.
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Science, 2006,
313,
1752-1756.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2006,
313,
1752-1756)
copyright 2006.
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Headers
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