2eeu: Difference between revisions

Revision as of 18:09, 21 February 2008

Guanine riboswitch U22A, A52U mutant bound to hypoxanthine

OverviewOverview

The purine riboswitch is one of a number of mRNA elements commonly found in the 5'-untranslated region capable of controlling expression in a cis-fashion via its ability to directly bind small-molecule metabolites. Extensive biochemical and structural analysis of the nucleobase-binding domain of the riboswitch, referred to as the aptamer domain, has revealed that the mRNA recognizes its cognate ligand using an intricately folded three-way junction motif that completely encapsulates the ligand. High-affinity binding of the purine nucleobase is facilitated by a distal loop-loop interaction that is conserved between both the adenine and guanine riboswitches. To understand the contribution of conserved nucleotides in both the three-way junction and the loop-loop interaction of this RNA, we performed a detailed mutagenic survey of these elements in the context of an adenine-responsive variant of the xpt-pbuX guanine riboswitch from Bacillus subtilis. The varying ability of these mutants to bind ligand as measured by isothermal titration calorimetry uncovered the conserved nucleotides whose identity is required for purine binding. Crystallographic analysis of the bound form of five mutants and chemical probing of their free state demonstrate that the identity of several universally conserved nucleotides is not essential for formation of the RNA-ligand complex but rather for maintaining a binding-competent form of the free RNA. These data show that conservation patterns in riboswitches arise from a combination of formation of the ligand-bound complex, promoting an open form of the free RNA, and participating in the secondary structural switch with the expression platform.

About this StructureAbout this Structure

2EEU is a Single protein structure of sequence from [1] with , and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Mutational analysis of the purine riboswitch aptamer domain., Gilbert SD, Love CE, Edwards AL, Batey RT, Biochemistry. 2007 Nov 20;46(46):13297-309. Epub 2007 Oct 26. PMID:17960911

Page seeded by OCA on Thu Feb 21 17:09:27 2008

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 ==Overview==
-The purine riboswitch is one of a number of mRNA elements commonly found, in the 5'-untranslated region capable of controlling expression in a, cis-fashion via its ability to directly bind small-molecule metabolites., Extensive biochemical and structural analysis of the nucleobase-binding, domain of the riboswitch, referred to as the aptamer domain, has revealed, that the mRNA recognizes its cognate ligand using an intricately folded, three-way junction motif that completely encapsulates the ligand., High-affinity binding of the purine nucleobase is facilitated by a distal, loop-loop interaction that is conserved between both the adenine and, guanine riboswitches. To understand the contribution of conserved, nucleotides in both the three-way junction and the loop-loop interaction, of this RNA, we performed a detailed mutagenic survey of these elements in, the context of an adenine-responsive variant of the xpt-pbuX guanine, riboswitch from Bacillus subtilis. The varying ability of these mutants to, bind ligand as measured by isothermal titration calorimetry uncovered the, conserved nucleotides whose identity is required for purine binding., Crystallographic analysis of the bound form of five mutants and chemical, probing of their free state demonstrate that the identity of several, universally conserved nucleotides is not essential for formation of the, RNA-ligand complex but rather for maintaining a binding-competent form of, the free RNA. These data show that conservation patterns in riboswitches, arise from a combination of formation of the ligand-bound complex, promoting an open form of the free RNA, and participating in the secondary, structural switch with the expression platform.
+The purine riboswitch is one of a number of mRNA elements commonly found in the 5'-untranslated region capable of controlling expression in a cis-fashion via its ability to directly bind small-molecule metabolites. Extensive biochemical and structural analysis of the nucleobase-binding domain of the riboswitch, referred to as the aptamer domain, has revealed that the mRNA recognizes its cognate ligand using an intricately folded three-way junction motif that completely encapsulates the ligand. High-affinity binding of the purine nucleobase is facilitated by a distal loop-loop interaction that is conserved between both the adenine and guanine riboswitches. To understand the contribution of conserved nucleotides in both the three-way junction and the loop-loop interaction of this RNA, we performed a detailed mutagenic survey of these elements in the context of an adenine-responsive variant of the xpt-pbuX guanine riboswitch from Bacillus subtilis. The varying ability of these mutants to bind ligand as measured by isothermal titration calorimetry uncovered the conserved nucleotides whose identity is required for purine binding. Crystallographic analysis of the bound form of five mutants and chemical probing of their free state demonstrate that the identity of several universally conserved nucleotides is not essential for formation of the RNA-ligand complex but rather for maintaining a binding-competent form of the free RNA. These data show that conservation patterns in riboswitches arise from a combination of formation of the ligand-bound complex, promoting an open form of the free RNA, and participating in the secondary structural switch with the expression platform.
 ==About this Structure==
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 Mutational analysis of the purine riboswitch aptamer domain., Gilbert SD, Love CE, Edwards AL, Batey RT, Biochemistry. 2007 Nov 20;46(46):13297-309. Epub 2007 Oct 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17960911 17960911]
 [[Category: Single protein]]
-[[Category: Batey, R.T.]]
+[[Category: Batey, R T.]]
-[[Category: Gilbert, S.D.]]
+[[Category: Gilbert, S D.]]
-[[Category: Love, C.E.]]
+[[Category: Love, C E.]]
 [[Category: ACT]]
 [[Category: HPA]]
@@ Line 26: / Line 26: @@
 [[Category: three-way junction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:56:21 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:09:27 2008''