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| | ==Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.== | | ==Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.== |
| - | <StructureSection load='6emv' size='340' side='right' caption='[[6emv]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='6emv' size='340' side='right'caption='[[6emv]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6emv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EMV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6emv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EMV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.9000144Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK0422 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311400 "Thermococcus kodakaraensis" Atomi et al. 2004])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=6emv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6emv OCA], [http://pdbe.org/6emv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6emv RCSB], [http://www.ebi.ac.uk/pdbsum/6emv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6emv 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=6emv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6emv OCA], [https://pdbe.org/6emv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6emv RCSB], [https://www.ebi.ac.uk/pdbsum/6emv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6emv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TRM10_THEKO TRM10_THEKO]] Catalyzes the S-adenosyl-L-methionine-dependent formation of either N(1)-methyladenine or N(1)-methylguanine at position 9 (m1A9 or m1G9) in tRNA.<ref>PMID:20525789</ref> | + | [https://www.uniprot.org/uniprot/TRM10_THEKO TRM10_THEKO] Catalyzes the S-adenosyl-L-methionine-dependent formation of either N(1)-methyladenine or N(1)-methylguanine at position 9 (m1A9 or m1G9) in tRNA.<ref>PMID:20525789</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 6emv" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6emv" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Thermococcus kodakaraensis atomi et al. 2004]] | + | [[Category: Large Structures]] |
| - | [[Category: Singh, R K]] | + | [[Category: Thermococcus kodakarensis]] |
| - | [[Category: Versees, W]] | + | [[Category: Singh RK]] |
| - | [[Category: Dual specificity enzyme]] | + | [[Category: Versees W]] |
| - | [[Category: Mtase]]
| + | |
| - | [[Category: Rna binding protein]]
| + | |
| - | [[Category: Spout]]
| + | |
| - | [[Category: Trm10]]
| + | |
| Structural highlights
Function
TRM10_THEKO Catalyzes the S-adenosyl-L-methionine-dependent formation of either N(1)-methyladenine or N(1)-methylguanine at position 9 (m1A9 or m1G9) in tRNA.[1]
Publication Abstract from PubMed
tRNA molecules get heavily modified posttranscriptionally. The N-1 methylation of purines at position 9 of eukaryal and archaeal tRNA is catalyzed by the SPOUT methyltranferase Trm10. Remarkably, while certain Trm10 orthologues are specific for either guanosine or adenosine, others show a dual specificity. Structural and functional studies have been performed on guanosine- and adenosine-specific enzymes. Here we report the structure and biochemical analysis of the dual specificity enzyme from Thermococcus kodakaraensis (TkTrm10). We report the first crystal structure of a construct of this enzyme, consisting of the N-terminal domain and the catalytic SPOUT domain. Moreover, crystal structures of the SPOUT domain, either in the apo form or bound to S-adenosyl-L-methionine or S-adenosyl-L-homocysteine reveal conformational plasticity of two active site loops upon substrate binding. Kinetic analysis shows that TkTrm10 has a high affinity for its tRNA substrates, while the enzyme on its own has a very low methyltransferase activity. Mutation of either of two active site aspartate residues (Asp206 and Asp245) to Asn or Ala results in only modest effects on the N-1 methylation reaction, with a small shift toward a preference for m(1)G formation over m(1)A formation. Only a double D206A/D245A mutation severely impairs activity. These results are in line with the recent finding that the single active-site aspartate was dispensable for activity in the guanosine-specific Trm10 from yeast, and suggest that also dual specificity Trm10 orthologues use a non-canonical tRNA methyltransferase mechanism without residues acting as general base catalysts.
Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism.,Singh RK, Feller A, Roovers M, Van Elder D, Wauters L, Droogmans L, Versees W RNA. 2018 May 30. pii: rna.064345.117. doi: 10.1261/rna.064345.117. PMID:29848639[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L. New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Nucleic Acids Res. 2010 Oct;38(19):6533-43. doi: 10.1093/nar/gkq451. Epub 2010, Jun 4. PMID:20525789 doi:http://dx.doi.org/10.1093/nar/gkq451
- ↑ Singh RK, Feller A, Roovers M, Van Elder D, Wauters L, Droogmans L, Versees W. Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism. RNA. 2018 May 30. pii: rna.064345.117. doi: 10.1261/rna.064345.117. PMID:29848639 doi:http://dx.doi.org/10.1261/rna.064345.117
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