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6emv

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==Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.==
==Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.==
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<StructureSection load='6emv' size='340' side='right' caption='[[6emv]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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<StructureSection load='6emv' size='340' side='right'caption='[[6emv]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6emv]] is a 3 chain structure. 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>
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<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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9000144&#8491;</td></tr>
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<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>
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<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>
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<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 ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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<ref>PMID:29848639</ref>
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==See Also==
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*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6emv" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Singh, R K]]
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[[Category: Large Structures]]
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[[Category: Versees, W]]
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[[Category: Thermococcus kodakarensis]]
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[[Category: Dual specificity enzyme]]
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[[Category: Singh RK]]
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[[Category: Mtase]]
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[[Category: Versees W]]
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[[Category: Rna binding protein]]
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[[Category: Spout]]
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[[Category: Trm10]]
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Current revision

Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.

PDB ID 6emv

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