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| | <StructureSection load='6q56' size='340' side='right'caption='[[6q56]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='6q56' size='340' side='right'caption='[[6q56]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6q56]] is a 4 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=6Q56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q56 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6q56]] is a 4 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=6Q56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q56 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trmK, yqfN, BSU25180 ([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=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(adenine(22)-N(1))-methyltransferase tRNA (adenine(22)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.217 2.1.1.217] </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=6q56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q56 OCA], [https://pdbe.org/6q56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q56 RCSB], [https://www.ebi.ac.uk/pdbsum/6q56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q56 ProSAT]</span></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=6q56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q56 OCA], [http://pdbe.org/6q56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q56 RCSB], [http://www.ebi.ac.uk/pdbsum/6q56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q56 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TRMK_BACSU TRMK_BACSU]] Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 22 (m1A22) in tRNA.<ref>PMID:18420655</ref> | + | [https://www.uniprot.org/uniprot/TRMK_BACSU TRMK_BACSU] Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 22 (m1A22) in tRNA.<ref>PMID:18420655</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6q56" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6q56" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Barraud, P]] | + | [[Category: Al Refaii A]] |
| - | [[Category: Brachet, F]] | + | [[Category: Barraud P]] |
| - | [[Category: Caillet, J]] | + | [[Category: Brachet F]] |
| - | [[Category: Degut, C]] | + | [[Category: Caillet J]] |
| - | [[Category: Droogmans, L]] | + | [[Category: Degut C]] |
| - | [[Category: Feller, A]] | + | [[Category: Droogmans L]] |
| - | [[Category: Larue, V]] | + | [[Category: Feller A]] |
| - | [[Category: Refaii, A Al]]
| + | [[Category: Larue V]] |
| - | [[Category: Roovers, M]] | + | [[Category: Roovers M]] |
| - | [[Category: Tisne, C]] | + | [[Category: Tisne C]] |
| - | [[Category: Methyltransferase]]
| + | |
| - | [[Category: Rna binding protein]]
| + | |
| - | [[Category: Trna methyltransferase]]
| + | |
| Structural highlights
Function
TRMK_BACSU Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 22 (m1A22) in tRNA.[1]
Publication Abstract from PubMed
1-Methyladenosine (m1A) is a modified nucleoside found at positions 9, 14, 22 and 58 of tRNAs, which arises from the transfer of a methyl group onto the N1-atom of adenosine. The yqfN gene of Bacillus subtilis encodes the methyltransferase TrmK (BsTrmK) responsible for the formation of m1A22 in tRNA. Here, we show that BsTrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A22. In addition to a non-Watson-Crick base-pair between the target A22 and a purine at position 13, the formation of m1A22 by BsTrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of BsTrmK showing an N-terminal catalytic domain harbouring the typical Rossmann-like fold of Class-I methyltransferases and a C-terminal coiled-coil domain. We used NMR chemical shift mapping to drive the docking of BstRNASer to BsTrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on BsTrmK mutants, both domains of BsTrmK participate in tRNA binding. BsTrmK recognises tRNA with very few structural changes in both partner, the non-Watson-Crick R13-A22 base-pair positioning the A22 N1-atom close to the SAM methyl group.
Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition.,Degut C, Roovers M, Barraud P, Brachet F, Feller A, Larue V, Al Refaii A, Caillet J, Droogmans L, Tisne C Nucleic Acids Res. 2019 Apr 1. pii: 5424071. doi: 10.1093/nar/gkz230. PMID:30931478[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM. The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK). Nucleic Acids Res. 2008 Jun;36(10):3252-62. doi: 10.1093/nar/gkn169. Epub 2008, Apr 17. PMID:18420655 doi:http://dx.doi.org/10.1093/nar/gkn169
- ↑ Degut C, Roovers M, Barraud P, Brachet F, Feller A, Larue V, Al Refaii A, Caillet J, Droogmans L, Tisne C. Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition. Nucleic Acids Res. 2019 Apr 1. pii: 5424071. doi: 10.1093/nar/gkz230. PMID:30931478 doi:http://dx.doi.org/10.1093/nar/gkz230
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