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==Crystal structure of the methyltransferase-ribozyme 1 (1-benzyl-adenosine derivative)== | ==Crystal structure of the methyltransferase-ribozyme 1 (1-benzyl-adenosine derivative)== | ||
<StructureSection load='7q7y' size='340' side='right'caption='[[7q7y]]' scene=''> | <StructureSection load='7q7y' size='340' side='right'caption='[[7q7y]], [[Resolution|resolution]] 2.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q7Y FirstGlance]. <br> | <table><tr><td colspan='2'>[[7q7y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q7Y FirstGlance]. <br> | ||
</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=7q7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q7y OCA], [https://pdbe.org/7q7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q7y RCSB], [https://www.ebi.ac.uk/pdbsum/7q7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q7y ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9SY:[(2R,3S,4R,5R)-5-[6-azanyl-1-(phenylmethyl)purin-1-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>9SY</scene>, <scene name='pdbligand=GUN:GUANINE'>GUN</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=7q7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q7y OCA], [https://pdbe.org/7q7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q7y RCSB], [https://www.ebi.ac.uk/pdbsum/7q7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q7y ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
RNA-catalyzed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyzes the site-specific synthesis of 1-methyladenosine (m(1)A) in RNA, using O(6)-methylguanine (m(6)G) as a methyl group donor. Here, we report the crystal structure of MTR1 at a resolution of 2.8 A, which reveals a guanine-binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m(1)A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution. | |||
Structure and mechanism of the methyltransferase ribozyme MTR1.,Scheitl CPM, Mieczkowski M, Schindelin H, Hobartner C Nat Chem Biol. 2022 May;18(5):547-555. doi: 10.1038/s41589-022-00976-x. Epub 2022, Mar 17. PMID:35301481<ref>PMID:35301481</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7q7y" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribozyme 3D structures|Ribozyme 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Synthetic construct]] | |||
[[Category: Hoebartner C]] | [[Category: Hoebartner C]] | ||
[[Category: Mieczkowski M]] | [[Category: Mieczkowski M]] | ||
Latest revision as of 16:15, 1 February 2024
Crystal structure of the methyltransferase-ribozyme 1 (1-benzyl-adenosine derivative)Crystal structure of the methyltransferase-ribozyme 1 (1-benzyl-adenosine derivative)
Structural highlights
Publication Abstract from PubMedRNA-catalyzed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyzes the site-specific synthesis of 1-methyladenosine (m(1)A) in RNA, using O(6)-methylguanine (m(6)G) as a methyl group donor. Here, we report the crystal structure of MTR1 at a resolution of 2.8 A, which reveals a guanine-binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m(1)A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution. Structure and mechanism of the methyltransferase ribozyme MTR1.,Scheitl CPM, Mieczkowski M, Schindelin H, Hobartner C Nat Chem Biol. 2022 May;18(5):547-555. doi: 10.1038/s41589-022-00976-x. Epub 2022, Mar 17. PMID:35301481[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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