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| | ==Crystal structure of S. pombe Dnmt2 methyltransferase== | | ==Crystal structure of S. pombe Dnmt2 methyltransferase== |
| - | <StructureSection load='6fdf' size='340' side='right' caption='[[6fdf]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='6fdf' size='340' side='right'caption='[[6fdf]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6fdf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FDF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6fdf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FDF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.697Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6fdd|6fdd]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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_(cytosine(38)-C(5))-methyltransferase tRNA (cytosine(38)-C(5))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.204 2.1.1.204] </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=6fdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdf OCA], [https://pdbe.org/6fdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fdf RCSB], [https://www.ebi.ac.uk/pdbsum/6fdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fdf 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=6fdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdf OCA], [http://pdbe.org/6fdf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fdf RCSB], [http://www.ebi.ac.uk/pdbsum/6fdf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fdf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PMT1M_SCHPO PMT1M_SCHPO]] Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp). Can also methylate cytosine 38 in tRNA(Glu), albeit to a lower level, but not tRNA(Lys). Pmt1-dependent tRNA methylation is induced by nitrogen limitation and depends on the nutrient-sensing protein kinase sck2. Does not have DNA-methylation activity.<ref>PMID:23074192</ref> | + | [https://www.uniprot.org/uniprot/PMT1M_SCHPO PMT1M_SCHPO] Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp). Can also methylate cytosine 38 in tRNA(Glu), albeit to a lower level, but not tRNA(Lys). Pmt1-dependent tRNA methylation is induced by nitrogen limitation and depends on the nutrient-sensing protein kinase sck2. Does not have DNA-methylation activity.<ref>PMID:23074192</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 6fdf" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6fdf" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ficner, R]] | + | [[Category: Large Structures]] |
| - | [[Category: Johannsson, S]] | + | [[Category: Schizosaccharomyces pombe]] |
| - | [[Category: Neumann, P]] | + | [[Category: Ficner R]] |
| - | [[Category: Dnmt2]]
| + | [[Category: Johannsson S]] |
| - | [[Category: Methyltransferase]]
| + | [[Category: Neumann P]] |
| - | [[Category: S-adenosylhomocysteine]] | + | |
| - | [[Category: Transferase]] | + | |
| - | [[Category: Trna]]
| + | |
| Structural highlights
Function
PMT1M_SCHPO Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp). Can also methylate cytosine 38 in tRNA(Glu), albeit to a lower level, but not tRNA(Lys). Pmt1-dependent tRNA methylation is induced by nitrogen limitation and depends on the nutrient-sensing protein kinase sck2. Does not have DNA-methylation activity.[1]
Publication Abstract from PubMed
Dnmt2 methylates cytosine at position 38 of tRNA(Asp) in a variety of eukaryotic organisms. A correlation between the presence of the hypermodified nucleoside queuosine (Q) at position 34 of tRNA(Asp) and the Dnmt2 dependent C38 methylation was recently found in vivo for S. pombe and D. discoideum. We demonstrate a direct effect of the Q-modification on the methyltransferase catalytic efficiency in vitro, as Vmax/K0.5 of purified S. pombe Dnmt2 shows an increase for in vitro transcribed tRNA(Asp) containing Q34 to 6.27 * 10(-3) s(-1) microM(-1) compared to 1.51 * 10(-3) s(-1) microM(-1) for the unmodified substrate. Q34tRNA(Asp) exhibits an only slightly increased affinity for Dnmt2 in comparison to unmodified G34tRNA. In order to get insight into the structural basis for the Q-dependency, the crystal structure of S. pombe Dnmt2 was determined at 1.7 A resolution. It closely resembles the known structures of human and E. histolytica Dnmt2, and contains the entire active site loop. The interaction with tRNA was analyzed by means of mass-spectrometry using UV cross-linked Dnmt2-tRNA complex. These cross-link data and computational docking of Dnmt2 and tRNA(Asp) reveal Q34 positioned adjacent to the S-adenosylmethionine occupying the active site, suggesting that the observed increase of Dnmt2 catalytic efficiency by queuine originates from optimal positioning of the substrate molecules and residues relevant for methyl transfer.
Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine.,Johannsson S, Neumann P, Wulf A, Welp LM, Gerber HD, Krull M, Diederichsen U, Urlaub H, Ficner R Sci Rep. 2018 Jun 11;8(1):8880. doi: 10.1038/s41598-018-27118-5. PMID:29892076[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Becker M, Muller S, Nellen W, Jurkowski TP, Jeltsch A, Ehrenhofer-Murray AE. Pmt1, a Dnmt2 homolog in Schizosaccharomyces pombe, mediates tRNA methylation in response to nutrient signaling. Nucleic Acids Res. 2012 Dec;40(22):11648-58. doi: 10.1093/nar/gks956. Epub 2012, Oct 15. PMID:23074192 doi:http://dx.doi.org/10.1093/nar/gks956
- ↑ Johannsson S, Neumann P, Wulf A, Welp LM, Gerber HD, Krull M, Diederichsen U, Urlaub H, Ficner R. Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine. Sci Rep. 2018 Jun 11;8(1):8880. doi: 10.1038/s41598-018-27118-5. PMID:29892076 doi:http://dx.doi.org/10.1038/s41598-018-27118-5
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