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| | ==Crystal Structure of TrmR from B. subtilis== | | ==Crystal Structure of TrmR from B. subtilis== |
| - | <StructureSection load='5zw3' size='340' side='right' caption='[[5zw3]], [[Resolution|resolution]] 2.27Å' scene=''> | + | <StructureSection load='5zw3' size='340' side='right'caption='[[5zw3]], [[Resolution|resolution]] 2.27Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZW3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZW3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></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]] 2.27Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yrrM, BSU27360 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=5zw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zw3 OCA], [http://pdbe.org/5zw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zw3 RCSB], [http://www.ebi.ac.uk/pdbsum/5zw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zw3 ProSAT]</span></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=5zw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zw3 OCA], [https://pdbe.org/5zw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zw3 RCSB], [https://www.ebi.ac.uk/pdbsum/5zw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zw3 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/TRMR_BACSU TRMR_BACSU] Catalyzes the methylation of 5-hydroxyuridine (ho5U) to form 5-methoxyuridine (mo5U) at position 34 in tRNAs.[HAMAP-Rule:MF_02217]<ref>PMID:29982645</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Almo, S C]] | + | [[Category: Large Structures]] |
| - | [[Category: Kim, J]] | + | [[Category: Almo SC]] |
| - | [[Category: Ryu, H]] | + | [[Category: Kim J]] |
| - | [[Category: Rna binding protein]] | + | [[Category: Ryu H]] |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
TRMR_BACSU Catalyzes the methylation of 5-hydroxyuridine (ho5U) to form 5-methoxyuridine (mo5U) at position 34 in tRNAs.[HAMAP-Rule:MF_02217][1]
Publication Abstract from PubMed
Derivatives of 5-hydroxyuridine (ho5U), such as 5-methoxyuridine (mo5U) and 5-oxyacetyluridine (cmo5U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the biosynthesis of cmo5U from ho5U involves the unique metabolite carboxy S-adenosylmethionine (Cx-SAM) and the carboxymethyl transferase CmoB. However, the equivalent position in the tRNA of Gram-positive bacteria is instead mo5U, where the methyl group is derived from SAM and installed by an unknown methyltransferase. By utilizing a cmoB-deficient strain of Escherichia coli as a host and assaying for the formation of mo5U in total RNA isolates with methyltransferases of unknown function from Bacillus subtilis, we found that this modification is installed by the enzyme TrmR (formerly known as YrrM). Furthermore, X-ray crystal structures of TrmR with and without the anticodon stemloop of tRNAAla have been determined, which provide insight into both sequence and structure specificity in the interactions of TrmR with tRNA.
Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine.,Ryu H, Grove TL, Almo SC, Kim J Nucleic Acids Res. 2018 Jun 30. pii: 5047278. doi: 10.1093/nar/gky592. PMID:29982645[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ryu H, Grove TL, Almo SC, Kim J. Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res. 2018 Jun 30. pii: 5047278. doi: 10.1093/nar/gky592. PMID:29982645 doi:http://dx.doi.org/10.1093/nar/gky592
- ↑ Ryu H, Grove TL, Almo SC, Kim J. Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res. 2018 Jun 30. pii: 5047278. doi: 10.1093/nar/gky592. PMID:29982645 doi:http://dx.doi.org/10.1093/nar/gky592
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