2eev: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2eev.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_2eev", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_2eev|  PDB=2eev  |  SCENE=  }}
'''Guanine riboswitch U22C, A52G mutant bound to hypoxanthine'''


==Guanine riboswitch U22C, A52G mutant bound to hypoxanthine==
<StructureSection load='2eev' size='340' side='right'caption='[[2eev]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2eev]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EEV FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2eev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eev OCA], [https://pdbe.org/2eev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eev RCSB], [https://www.ebi.ac.uk/pdbsum/2eev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eev ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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<ref>PMID:17960911</ref>
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==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2EEV is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EEV OCA].
</div>
<div class="pdbe-citations 2eev" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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://www.ncbi.nlm.nih.gov/pubmed/17960911 17960911]
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
[[Category: Single protein]]
== References ==
[[Category: Batey, R T.]]
<references/>
[[Category: Gilbert, S D.]]
__TOC__
[[Category: Love, C E.]]
</StructureSection>
[[Category: Base triple]]
[[Category: Bacillus subtilis]]
[[Category: Double helix]]
[[Category: Large Structures]]
[[Category: Guanine]]
[[Category: Batey RT]]
[[Category: Hypoxanthine]]
[[Category: Gilbert SD]]
[[Category: Mrna]]
[[Category: Love CE]]
[[Category: Riboswitch]]
[[Category: Rna-ligand complex]]
[[Category: Three-way junction]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 02:26:50 2008''

Latest revision as of 21:44, 20 September 2023

Guanine riboswitch U22C, A52G mutant bound to hypoxanthineGuanine riboswitch U22C, A52G mutant bound to hypoxanthine

Structural highlights

2eev is a 1 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Gilbert SD, Love CE, Edwards AL, Batey RT. Mutational analysis of the purine riboswitch aptamer domain. Biochemistry. 2007 Nov 20;46(46):13297-309. Epub 2007 Oct 26. PMID:17960911 doi:10.1021/bi700410g

2eev, resolution 1.95Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2eev&oldid=3880524"