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==Structure of the SAM-I/IV riboswitch (env87(deltaU92))==
==Structure of the SAM-I/IV riboswitch (env87(deltaU92))==
<StructureSection load='4oqu' size='340' side='right' caption='[[4oqu]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
<StructureSection load='4oqu' size='340' side='right'caption='[[4oqu]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4oqu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQU FirstGlance]. <br>
<table><tr><td colspan='2'>[[4oqu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Metagenome Metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQU FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene><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]] 3.2&#8491;</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4oqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqu RCSB], [http://www.ebi.ac.uk/pdbsum/4oqu PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
<table>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4oqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqu OCA], [https://pdbe.org/4oqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqu RCSB], [https://www.ebi.ac.uk/pdbsum/4oqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqu ProSAT]</span></td></tr>
<div style="background-color:#fffaf0;">
</table>
== Publication Abstract from PubMed ==
In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.
 
Structural basis for diversity in the SAM clan of riboswitches.,Trausch JJ, Xu Z, Edwards AL, Reyes FE, Ross PE, Knight R, Batey RT Proc Natl Acad Sci U S A. 2014 May 6;111(18):6624-9. doi:, 10.1073/pnas.1312918111. Epub 2014 Apr 21. PMID:24753586<ref>PMID:24753586</ref>


From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Batey, R T.]]
[[Category: Large Structures]]
[[Category: Edwards, A L.]]
[[Category: Metagenome]]
[[Category: Reyes, F E.]]
[[Category: Batey RT]]
[[Category: Trausch, J J.]]
[[Category: Edwards AL]]
[[Category: Aptamer]]
[[Category: Reyes FE]]
[[Category: Pseudoknot]]
[[Category: Trausch JJ]]
[[Category: Regulation]]
[[Category: Riboswitch]]
[[Category: Rna]]
[[Category: S-adenosylmethionine]]

Latest revision as of 15:41, 1 March 2024

Structure of the SAM-I/IV riboswitch (env87(deltaU92))Structure of the SAM-I/IV riboswitch (env87(deltaU92))

Structural highlights

4oqu is a 1 chain structure with sequence from Metagenome. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

4oqu, resolution 3.20Å

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OCA
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