2dul - Revision history

OCA at 13:48, 13 March 2024

2024-03-13T13:48:18Z

← Older revision		Revision as of 13:48, 13 March 2024
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	<StructureSection load='2dul' size='340' side='right'caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dul' size='340' side='right'caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~'pyrococcus_shinkaii' 'pyrococcus shinkaii'~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUL FirstGlance]. <br>
	</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>~~</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]] 1.9Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>trm1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~53953 'Pyrococcus shinkaii'])</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></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Transferase Transferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </~~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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [https://pdbe.org/2dul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [https://www.ebi.ac.uk/pdbsum/2dul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dul ProSAT], [https://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [https://pdbe.org/2dul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [https://www.ebi.ac.uk/pdbsum/2dul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dul ProSAT], [https://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/TRM1_PYRHO TRM1_PYRHO]] Dimethylates a single guanine residue at position 26 of a number of tRNAs using S-adenosyl-L-methionine as donor of the methyl groups (By similarity).		[https://www.uniprot.org/uniprot/TRM1_PYRHO TRM1_PYRHO] Dimethylates a single guanine residue at position 26 of a number of tRNAs using S-adenosyl-L-methionine as donor of the methyl groups (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dul ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dul ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Trm1 catalyzes a two-step reaction, leading to mono- and dimethylation of guanosine at position 26 in most eukaryotic and archaeal tRNAs. We report the crystal structures of Trm1 from Pyrococcus horikoshii liganded with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine. The protein comprises N-terminal and C-terminal domains with class I methyltransferase and novel folds, respectively. The methyl moiety of S-adenosyl-l-methionine points toward the invariant Phe27 and Phe140 within a narrow pocket, where the target G26 might flip in. Mutagenesis of Phe27 or Phe140 to alanine abolished the enzyme activity, indicating their role in methylating G26. Structural analyses revealed that the movements of Phe140 and the loop preceding Phe27 may be involved in dissociation of the monomethylated tRNA*Trm1 complex prior to the second methylation. Moreover, the catalytic residues Asp138, Pro139, and Phe140 are in a different motif from that in DNA 6-methyladenosine methyltransferases, suggesting a different methyl transfer mechanism in the Trm1 family.

	Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.,Ihsanawati, Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S J Mol Biol. 2008 Nov 21;383(4):871-84. Epub 2008 Sep 5. PMID:18789948<ref>PMID:18789948</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2dul" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Pyrococcus shinkaii]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Transferase~~]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bessho, Y]]		[[Category: Bessho Y]]
	[[Category: Ihsanawati]]		[[Category: Ihsanawati]]
	~~[[Category: Structural genomic]]~~		[[Category: Shirouzu M]]
	[[Category: Shirouzu, M]]		[[Category: Yokoyama S]]
	[[Category: Yokoyama, S]]
	~~[[Category: Guanine 26]]~~
	~~[[Category: National project on protein structural and functional analyse]]~~
	~~[[Category: Nppsfa]]~~
	~~[[Category: Rsgi]]~~
	~~[[Category: Trna modification enzyme~~]]

OCA at 11:37, 10 February 2021

2021-02-10T11:37:58Z

← Older revision		Revision as of 11:37, 10 February 2021
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	==Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii==		==Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii==
	<StructureSection load='2dul' size='340' side='right' caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dul' size='340' side='right'caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUL 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></td></tr>		</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></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Transferase Transferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Transferase Transferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [~~http~~://pdbe.org/2dul PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dul PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dul ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [https://pdbe.org/2dul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [https://www.ebi.ac.uk/pdbsum/2dul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dul ProSAT], [https://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/TRM1_PYRHO TRM1_PYRHO]] Dimethylates a single guanine residue at position 26 of a number of tRNAs using S-adenosyl-L-methionine as donor of the methyl groups (By similarity).		[[https://www.uniprot.org/uniprot/TRM1_PYRHO TRM1_PYRHO]] Dimethylates a single guanine residue at position 26 of a number of tRNAs using S-adenosyl-L-methionine as donor of the methyl groups (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus shinkaii]]		[[Category: Pyrococcus shinkaii]]
			[[Category: Large Structures]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Bessho, Y]]		[[Category: Bessho, Y]]

OCA at 07:13, 6 June 2018

2018-06-06T07:13:02Z

← Older revision		Revision as of 07:13, 6 June 2018
Line 1:		Line 1:

	==Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii==		==Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii==
	<StructureSection load='2dul' size='340' side='right' caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dul' size='340' side='right' caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [http://pdbe.org/2dul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [http://www.ebi.ac.uk/pdbsum/2dul PDBsum], [http://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [http://pdbe.org/2dul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [http://www.ebi.ac.uk/pdbsum/2dul PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dul ProSAT], [http://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dul_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dul_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 12:16, 9 February 2016

2016-02-09T12:16:48Z

← Older revision		Revision as of 12:16, 9 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dul ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:10, 10 September 2015

2015-09-10T22:10:21Z

← Older revision		Revision as of 22:10, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dul' size='340' side='right' caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dul' size='340' side='right' caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii Pyrococcus horikoshii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUL 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></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus ~~horikoshii~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~tRNA_(guanine-N(2)-)-methyltransferase tRNA (guanine-N(2)-)-methyltransferase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.32 2.1.1.32] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [http://www.ebi.ac.uk/pdbsum/2dul PDBsum], [http://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [http://pdbe.org/2dul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [http://www.ebi.ac.uk/pdbsum/2dul PDBsum], [http://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2dul" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus ~~horikoshii~~]]		[[Category: Pyrococcus shinkaii]]
			[[Category: Transferase]]
	[[Category: Bessho, Y]]		[[Category: Bessho, Y]]
	[[Category: Ihsanawati]]		[[Category: Ihsanawati]]
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	[[Category: Nppsfa]]		[[Category: Nppsfa]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	~~[[Category: Transferase]]~~
	[[Category: Trna modification enzyme]]		[[Category: Trna modification enzyme]]

OCA at 06:45, 25 December 2014

2014-12-25T06:45:37Z

← Older revision		Revision as of 06:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUL FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine-N(2)-)-methyltransferase tRNA (guanine-N(2)-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.32 2.1.1.32] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine-N(2)-)-methyltransferase tRNA (guanine-N(2)-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.32 2.1.1.32] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [http://www.ebi.ac.uk/pdbsum/2dul PDBsum], [http://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</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=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [http://www.ebi.ac.uk/pdbsum/2dul PDBsum], [http://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/TRM1_PYRHO TRM1_PYRHO]] Dimethylates a single guanine residue at position 26 of a number of tRNAs using S-adenosyl-L-methionine as donor of the methyl groups (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bessho, Y.]]		[[Category: Bessho, Y]]
	[[Category: Ihsanawati]]		[[Category: Ihsanawati]]
	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]		[[Category: Structural genomic]]
	[[Category: Shirouzu, M.]]		[[Category: Shirouzu, M]]
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S]]
	[[Category: Guanine 26]]		[[Category: Guanine 26]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
	~~[[Category: Riken structural genomics/proteomics initiative]]~~
	[[Category: Rsgi]]		[[Category: Rsgi]]
	~~[[Category: Structural genomic]]~~
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trna modification enzyme]]		[[Category: Trna modification enzyme]]

OCA at 03:02, 30 September 2014

2014-09-30T03:02:44Z

← Older revision		Revision as of 03:02, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2dul~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii==
			<StructureSection load='2dul' size='340' side='right' caption='[[2dul]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DUL FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine-N(2)-)-methyltransferase tRNA (guanine-N(2)-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.32 2.1.1.32] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dul OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dul RCSB], [http://www.ebi.ac.uk/pdbsum/2dul PDBsum], [http://www.topsan.org/Proteins/RSGI/2dul TOPSAN]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2dul_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Trm1 catalyzes a two-step reaction, leading to mono- and dimethylation of guanosine at position 26 in most eukaryotic and archaeal tRNAs. We report the crystal structures of Trm1 from Pyrococcus horikoshii liganded with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine. The protein comprises N-terminal and C-terminal domains with class I methyltransferase and novel folds, respectively. The methyl moiety of S-adenosyl-l-methionine points toward the invariant Phe27 and Phe140 within a narrow pocket, where the target G26 might flip in. Mutagenesis of Phe27 or Phe140 to alanine abolished the enzyme activity, indicating their role in methylating G26. Structural analyses revealed that the movements of Phe140 and the loop preceding Phe27 may be involved in dissociation of the monomethylated tRNA*Trm1 complex prior to the second methylation. Moreover, the catalytic residues Asp138, Pro139, and Phe140 are in a different motif from that in DNA 6-methyladenosine methyltransferases, suggesting a different methyl transfer mechanism in the Trm1 family.

	~~{{STRUCTURE_2dul\| PDB=2dul \| SCENE= }}~~		Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.,Ihsanawati, Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S J Mol Biol. 2008 Nov 21;383(4):871-84. Epub 2008 Sep 5. PMID:18789948<ref>PMID:18789948</ref>

	~~===Crystal structure~~ of ~~tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18789948}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dul]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018789948<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bessho, Y.]]		[[Category: Bessho, Y.]]

OCA: Protected "2dul" [edit=sysop:move=sysop]

2013-01-06T12:12:42Z

Protected "2dul" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:12, 6 January 2013
(No difference)

OCA at 12:12, 6 January 2013

2013-01-06T12:12:41Z

← Older revision		Revision as of 12:12, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2dul.png\|left\|200px]]		[[Image:2dul.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dul", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2dul\| PDB=2dul \| SCENE= }}		{{STRUCTURE_2dul\| PDB=2dul \| SCENE= }}

	===Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii===		===Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18789948}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18789948 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18789948}}		{{ABSTRACT_PUBMED_18789948}}

	==About this Structure==		==About this Structure==
	~~2DUL~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA].		[[2dul]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUL OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18789948~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018789948</ref><references group="xtra"/>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bessho, Y.]]		[[Category: Bessho, Y.]]
Line 36:		Line 24:
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
			[[Category: Transferase]]
	[[Category: Trna modification enzyme]]		[[Category: Trna modification enzyme]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:42:52 2009''~~

OCA at 07:42, 17 February 2009

2009-02-17T07:42:53Z

← Older revision		Revision as of 07:42, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
	Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii., Ihsanawati, Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S, J Mol Biol. 2008 Nov 21;383(4):871-84. Epub 2008 Sep 5. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18789948 18789948]~~		<ref group="xtra">PMID:18789948</ref><references group="xtra"/>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bessho, Y.]]		[[Category: Bessho, Y.]]
Line 38:		Line 38:
	[[Category: Trna modification enzyme]]		[[Category: Trna modification enzyme]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 18~~:47:~~45 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:42:52 2009''