6emv: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 6emv is ~~ON HOLD~~ ~~until Paper~~ Publication

==Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.==

== Structural highlights ==

<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>

</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>

<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>

</table>

== 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>

== 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.

~~Authors:~~ Singh, ~~R.K.~~, Versees, W.

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>

~~Description: Crystal Structure~~ of ~~dual specific Trm10 construct from Thermococcus kodakaraensis~~.

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~[[Category~~: ~~Unreleased Structures]]~~

</div>

[[Category: Singh, R.K]]

== References ==

__TOC__

</StructureSection>

[[Category: Singh, R K]]

[[Category: Versees, W]]

[[Category: Dual specificity enzyme]]

[[Category: Mtase]]

[[Category: Rna binding protein]]

[[Category: Spout]]

[[Category: Trm10]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6emv is ON HOLD  until Paper Publication
+==Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.==
+<StructureSection load='6emv' size='340' side='right' caption='[[6emv]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+</table>
+== 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>
+<div style="background-color:#fffaf0;">
+== 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.
-Authors: Singh, R.K., Versees, W.
+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>
-Description: Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Singh, R.K]]
+<div class="pdbe-citations 6emv" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Singh, R K]]
 [[Category: Versees, W]]
+[[Category: Dual specificity enzyme]]
+[[Category: Mtase]]
+[[Category: Rna binding protein]]
+[[Category: Spout]]
+[[Category: Trm10]]