6las: Difference between revisions
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==the wildtype SAM-VI riboswitch bound to SAM== | |||
<StructureSection load='6las' size='340' side='right'caption='[[6las]], [[Resolution|resolution]] 2.71Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6las]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6LAS FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6las FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6las OCA], [http://pdbe.org/6las PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6las RCSB], [http://www.ebi.ac.uk/pdbsum/6las PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6las ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Riboswitches are metabolite-sensing, conserved domains located in non-coding regions of mRNA that are central to regulation of gene expression. Here we report the first three-dimensional structure of the recently discovered S-adenosyl-L-methionine responsive SAM-VI riboswitch. SAM-VI adopts a unique fold and ligand pocket that are distinct from all other known SAM riboswitch classes. The ligand binds to the junctional region with its adenine tightly intercalated and Hoogsteen base-paired. Furthermore, we reveal the ligand discrimination mode of SAM-VI by additional X-ray structures of this riboswitch bound to S-adenosyl-L-homocysteine and a synthetic ligand mimic, in combination with isothermal titration calorimetry and fluorescence spectroscopy to explore binding thermodynamics and kinetics. The structure is further evaluated by analysis of ligand binding to SAM-VI mutants. It thus provides a thorough basis for developing synthetic SAM cofactors for applications in chemical and synthetic RNA biology. | |||
SAM-VI riboswitch structure and signature for ligand discrimination.,Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A Nat Commun. 2019 Dec 16;10(1):5728. doi: 10.1038/s41467-019-13600-9. PMID:31844059<ref>PMID:31844059</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6las" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Ren, A]] | [[Category: Ren, A]] | ||
[[Category: Sun, A]] | [[Category: Sun, A]] | ||
[[Category: Riboswitch]] | |||
[[Category: Rna]] | |||
[[Category: Rna binding protein-rna complex]] | |||
[[Category: Sam]] | |||
[[Category: Sam-vi]] | |||
Revision as of 11:19, 1 January 2020
the wildtype SAM-VI riboswitch bound to SAMthe wildtype SAM-VI riboswitch bound to SAM
Structural highlights
Function[SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.[1] Publication Abstract from PubMedRiboswitches are metabolite-sensing, conserved domains located in non-coding regions of mRNA that are central to regulation of gene expression. Here we report the first three-dimensional structure of the recently discovered S-adenosyl-L-methionine responsive SAM-VI riboswitch. SAM-VI adopts a unique fold and ligand pocket that are distinct from all other known SAM riboswitch classes. The ligand binds to the junctional region with its adenine tightly intercalated and Hoogsteen base-paired. Furthermore, we reveal the ligand discrimination mode of SAM-VI by additional X-ray structures of this riboswitch bound to S-adenosyl-L-homocysteine and a synthetic ligand mimic, in combination with isothermal titration calorimetry and fluorescence spectroscopy to explore binding thermodynamics and kinetics. The structure is further evaluated by analysis of ligand binding to SAM-VI mutants. It thus provides a thorough basis for developing synthetic SAM cofactors for applications in chemical and synthetic RNA biology. SAM-VI riboswitch structure and signature for ligand discrimination.,Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A Nat Commun. 2019 Dec 16;10(1):5728. doi: 10.1038/s41467-019-13600-9. PMID:31844059[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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