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9xzr
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Trm10-tRNA complex (open conformation)== | |
| + | <StructureSection load='9xzr' size='340' side='right'caption='[[9xzr]], [[Resolution|resolution]] 3.37Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[9xzr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_BMN1-35 Saccharomyces cerevisiae BMN1-35]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9XZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9XZR FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.37Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AN6:5-{[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)AMINO}-5-DEOXYADENOSINE'>AN6</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=9xzr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9xzr OCA], [https://pdbe.org/9xzr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9xzr RCSB], [https://www.ebi.ac.uk/pdbsum/9xzr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9xzr ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/TRM10_YEAST TRM10_YEAST] Catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs.<ref>PMID:12702816</ref> <ref>PMID:15640439</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The evolutionarily conserved methyltransferase Trm10 modifies the N1 position of guanosine 9 (G9) in some tRNAs, but how the enzyme recognizes and modifies its substrate tRNAs remains unclear. Here, we used an S-adenosyl-L-methionine (SAM) analog to trap the Trm10-tRNA(Gly) complex and enable determination of its structure in a post-catalytic state by cryogenic electron microscopy (cryo-EM). We observed three distinct complexes: two with a single Trm10 bound to tRNA that differ in their tRNA acceptor stem orientation ("closed" and "open") and a minor population with two Trm10s engaging the same tRNA. The monomeric complexes reveal a positively charged surface that guides the G9 into the catalytic site with key conserved residues forming "pincer"-like interactions that stabilize the flipped methylated nucleotide. In the open tRNA conformation, the acceptor stem is rotated away from the enzyme, weakening the tRNA-protein contacts, consistent with a product-release conformation. The dimeric complex, which is supported by tRNA-dependent protein crosslinking, reveals one Trm10 positioned similarly to the monomeric complexes and engaged with G9, while the other Trm10 contacts distal tRNA regions, suggesting a potential role in facilitating a key conformational transition during the process of catalysis or modified tRNA release. Finally, molecular dynamics simulations comparing G9- and A9-containing complexes reveal that G9 is efficiently stabilized in the binding pocket unlike A9, identifying the structural basis for guanosine selectivity. Overall, these findings reveal the structural determinants of G9-specific tRNA methylation by Trm10 and suggest a unique mechanism of action among RNA-modifying SPOUT methyltransferases. | ||
| - | + | Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10.,Nandi S, Strassler SE, Dey D, Krishnamohan A, Harris GM, Comstock LR, Jackman JE, Conn GL bioRxiv [Preprint]. 2025 Dec 14:2025.12.12.694034. doi: , 10.64898/2025.12.12.694034. PMID:41427370<ref>PMID:41427370</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 9xzr" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Saccharomyces cerevisiae]] | ||
| + | [[Category: Saccharomyces cerevisiae BMN1-35]] | ||
| + | [[Category: Conn GL]] | ||
| + | [[Category: Nandi S]] | ||
| + | [[Category: Strassler SE]] | ||
Current revision
Trm10-tRNA complex (open conformation)
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