4l81: Difference between revisions
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The | ==Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93))== | ||
<StructureSection load='4l81' size='340' side='right'caption='[[4l81]], [[Resolution|resolution]] 2.95Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4l81]] 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=4L81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L81 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]] 2.95Å</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=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=4l81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l81 OCA], [https://pdbe.org/4l81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l81 RCSB], [https://www.ebi.ac.uk/pdbsum/4l81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l81 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== 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> | |||
</div> | |||
<div class="pdbe-citations 4l81" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Metagenome]] | |||
[[Category: Batey RT]] | |||
[[Category: Edwards AL]] | |||
[[Category: Reyes FE]] | |||
[[Category: Trausch JJ]] | |||
Latest revision as of 19:14, 20 September 2023
Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93))Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93))
Structural highlights
Publication Abstract from PubMedIn 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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