6laz: Difference between revisions
New page: '''Unreleased structure''' The entry 6laz is ON HOLD until Paper Publication Authors: Ren, A., Sun, A. Description: the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 [[... |
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==the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1== | |||
<StructureSection load='6laz' size='340' side='right'caption='[[6laz]], [[Resolution|resolution]] 2.76Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6laz]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_angulatum Bifidobacterium angulatum] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LAZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LAZ 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]] 2.76Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E7X:(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate'>E7X</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6laz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6laz OCA], [https://pdbe.org/6laz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6laz RCSB], [https://www.ebi.ac.uk/pdbsum/6laz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6laz ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://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> | ||
[[Category: Ren | <div class="pdbe-citations 6laz" style="background-color:#fffaf0;"></div> | ||
[[Category: Sun | |||
==See Also== | |||
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]] | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bifidobacterium angulatum]] | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Ren A]] | |||
[[Category: Sun A]] | |||
Latest revision as of 13:54, 22 November 2023
the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1
Structural highlights
FunctionSNRPA_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. See AlsoReferences
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