1y5w - Revision history

OCA at 08:10, 25 October 2023

OCA — Wed, 25 Oct 2023 08:10:20 GMT

←Older revision		Revision as of 08:10, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1y5w' size='340' side='right'caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='1y5w' size='340' side='right'caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_anaerobium"_(sic)_shimwell_1937 "achromobacter anaerobium" (sic) shimwell 1937~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Y5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y5W 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>, <scene name='pdbligand=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.58Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</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=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 "Achromobacter anaerobium" (sic) Shimwell 1937])</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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [https://pdbe.org/1y5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [https://www.ebi.ac.uk/pdbsum/1y5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5w ProSAT]</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(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [~~http~~://pdbe.org/1y5w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1y5w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5w ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO]] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]	+	[https://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]	+	*[[TRNA-guanine transglycosylase 3D structures\|TRNA-guanine transglycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brenk, R]]	+	[[Category: Zymomonas mobilis]]
-	[[Category: Diederich, F]]	+	[[Category: Brenk R]]
-	[[Category: Heine, A]]	+	[[Category: Diederich F]]
-	[[Category: Klebe, G]]	+	[[Category: Heine A]]
-	[[Category: Meyer~~, E A~~]]	+	[[Category: Klebe G]]
-	[[Category: Stengl, B]]	+	[[Category: Meyer EA]]
-	~~[[Category: Transferase~~]]	+	[[Category: Stengl B]]

OCA at 06:26, 19 August 2020

OCA — Wed, 19 Aug 2020 06:26:32 GMT

←Older revision		Revision as of 06:26, 19 August 2020
Line 1:		Line 1:

	==tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==		==tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==
-	<StructureSection load='1y5w' size='340' side='right' caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='1y5w' size='340' side='right'caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_anaerobium"_(sic)_shimwell_1937 "achromobacter anaerobium" (sic) shimwell 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Y5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_anaerobium"_(sic)_shimwell_1937 "achromobacter anaerobium" (sic) shimwell 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Y5W 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=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 "Achromobacter anaerobium" (sic) Shimwell 1937])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 "Achromobacter anaerobium" (sic) Shimwell 1937])</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(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://pdbe.org/1y5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5w ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://pdbe.org/1y5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Brenk, R]]		[[Category: Brenk, R]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]

OCA at 06:42, 25 April 2018

OCA — Wed, 25 Apr 2018 06:42:48 GMT

←Older revision		Revision as of 06:42, 25 April 2018
Line 1:		Line 1:
		+
	==tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==		==tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==
	<StructureSection load='1y5w' size='340' side='right' caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='1y5w' size='340' side='right' caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 "Achromobacter anaerobium" (sic) Shimwell 1937])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 "Achromobacter anaerobium" (sic) Shimwell 1937])</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(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://pdbe.org/1y5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum]</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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://pdbe.org/1y5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y5/1y5w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y5/1y5w_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 07:51, 9 February 2016

OCA — Tue, 09 Feb 2016 07:51:01 GMT

←Older revision		Revision as of 07:51, 9 February 2016
Line 19:		Line 19:
	<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=1y5w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:08, 10 September 2015

OCA — Thu, 10 Sep 2015 20:08:26 GMT

←Older revision		Revision as of 20:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1y5w' size='340' side='right' caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='1y5w' size='340' side='right' caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Zymomonas_mobilis Zymomonas mobilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_anaerobium"_(sic)_shimwell_1937 "achromobacter anaerobium" (sic) shimwell 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y5W 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=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 ~~Zymomonas mobilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 "Achromobacter anaerobium" (sic) Shimwell 1937])</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_transglycosylase~~ tRNA-guanine transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum]</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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://pdbe.org/1y5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1y5w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Zymomonas mobilis]]
-	[[Category: TRNA-guanine transglycosylase]]
	[[Category: Brenk, R]]		[[Category: Brenk, R]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]

OCA at 05:30, 25 December 2014

OCA — Thu, 25 Dec 2014 05:30:10 GMT

←Older revision		Revision as of 05:30, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y5W FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y5W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 Zymomonas mobilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 Zymomonas mobilis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA-guanine_transglycosylase tRNA-guanine transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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_transglycosylase tRNA-guanine transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum]</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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO]] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Zymomonas mobilis]]		[[Category: Zymomonas mobilis]]
	[[Category: TRNA-guanine transglycosylase]]		[[Category: TRNA-guanine transglycosylase]]
-	[[Category: Brenk, R.]]	+	[[Category: Brenk, R]]
-	[[Category: Diederich, F.]]	+	[[Category: Diederich, F]]
-	[[Category: Heine, A.]]	+	[[Category: Heine, A]]
-	[[Category: Klebe, G.]]	+	[[Category: Klebe, G]]
-	[[Category: Meyer, E A.]]	+	[[Category: Meyer, E A]]
-	[[Category: Stengl, B.]]	+	[[Category: Stengl, B]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 20:57, 29 September 2014

OCA — Mon, 29 Sep 2014 20:57:03 GMT

←Older revision		Revision as of 20:57, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1y5w.~~png~~\|~~left~~\|200px]]	+	==tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one==
		+	<StructureSection load='1y5w' size='340' side='right' caption='[[1y5w]], [[Resolution\|resolution]] 1.58Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y5W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NEZ:6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>NEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q4w\|1q4w]], [[1r5y\|1r5y]], [[1s38\|1s38]], [[1q63\|1q63]], [[1q65\|1q65]], [[1q66\|1q66]], [[1y5v\|1y5v]], [[1y5x\|1y5x]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 Zymomonas mobilis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA-guanine_transglycosylase tRNA-guanine transglycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=1y5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y5w RCSB], [http://www.ebi.ac.uk/pdbsum/1y5w PDBsum]</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/y5/1y5w_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 ==
		+	The bacterial tRNA-guanine transglycosylase (TGT) is a tRNA modifying enzyme catalyzing the exchange of guanine 34 by the modified base preQ1. The enzyme is involved in the infection pathway of Shigella, causing bacterial dysentery. As no crystal structure of the Shigella enzyme is available the homologous Zymomonas mobilis TGT was used for structure-based drug design resulting in new, potent, lin-benzoguanine-based inhibitors. Thorough kinetic studies show size-dependent inhibition of these compounds resulting in either a competitive or non-competitive blocking of the base exchange reaction in the low micromolar range. Four crystal structures of TGT-inhibitor complexes were determined with a resolution of 1.58-2.1 A. These structures give insight into the structural flexibility of TGT necessary to perform catalysis. In three of the structures molecular rearrangements are observed that match with conformational changes also noticed upon tRNA substrate binding. Several water molecules are involved in these rearrangement processes. Two of them demonstrate the structural and catalytic importance of water molecules during TGT base exchange reaction. In the fourth crystal structure the inhibitor unexpectedly interferes with protein contact formation and crystal packing. In all presently known TGT crystal structures the enzyme forms tightly associated homodimers internally related by crystallographic symmetry. Upon binding of the fourth inhibitor the dimer interface, however, becomes partially disordered. This result prompted further analyses to investigate the relevance of dimer formation for the functional protein. Consultation of the available TGT structures and sequences from different species revealed structural and functional conservation across the contacting residues. This suggests that bacterial and eukaryotic TGT could possibly act as homodimers in catalysis. It is hypothesized that one unit of the dimer performs the catalytic reaction whereas the second is required to recognize and properly orient the bound tRNA for the catalytic reaction.

-	~~{{STRUCTURE_1y5w\| PDB=1y5w \| SCENE= }}~~	+	Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding.,Stengl B, Meyer EA, Heine A, Brenk R, Diederich F, Klebe G J Mol Biol. 2007 Jul 13;370(3):492-511. Epub 2007 Apr 12. PMID:17524419<ref>PMID:17524419</ref>

-	~~===tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1~~,~~7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_17524419}}~~	+	==See Also==
-		+	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1y5w~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:017524419<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Zymomonas mobilis]]		[[Category: Zymomonas mobilis]]
	[[Category: TRNA-guanine transglycosylase]]		[[Category: TRNA-guanine transglycosylase]]

OCA: Protected "1y5w" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:54:37 GMT

Protected "1y5w" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:54, 5 January 2013

OCA at 11:54, 5 January 2013

OCA — Sat, 05 Jan 2013 11:54:35 GMT

←Older revision		Revision as of 11:54, 5 January 2013
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-	{{Seed}}
	[[Image:1y5w.png\|left\|200px]]		[[Image:1y5w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1y5w", 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_1y5w\| PDB=1y5w \| SCENE= }}		{{STRUCTURE_1y5w\| PDB=1y5w \| SCENE= }}

	===tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one===		===tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17524419}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17524419 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17524419}}		{{ABSTRACT_PUBMED_17524419}}

	==About this Structure==		==About this Structure==
-	~~1Y5W~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA].	+	[[1y5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17524419~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017524419</ref><references group="xtra"/>
-	~~[[Category: Queuine tRNA-ribosyltransferase]]~~	+
	[[Category: Zymomonas mobilis]]		[[Category: Zymomonas mobilis]]
		+	[[Category: TRNA-guanine transglycosylase]]
	[[Category: Brenk, R.]]		[[Category: Brenk, R.]]
	[[Category: Diederich, F.]]		[[Category: Diederich, F.]]
Line 33:		Line 21:
	[[Category: Stengl, B.]]		[[Category: Stengl, B.]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 09:24:45 2009''

OCA at 06:24, 6 May 2009

OCA — Wed, 06 May 2009 06:24:46 GMT

←Older revision		Revision as of 06:24, 6 May 2009
Line 12:		Line 12:
	===tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one===		===tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_17524419}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17524419 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17524419}}

	==About this Structure==		==About this Structure==
	1Y5W is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA].		1Y5W is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5W OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:17524419</ref><references group="xtra"/>
	[[Category: Queuine tRNA-ribosyltransferase]]		[[Category: Queuine tRNA-ribosyltransferase]]
	[[Category: Zymomonas mobilis]]		[[Category: Zymomonas mobilis]]
Line 25:		Line 34:
	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 08~~:07:04 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 09:24:45 2009''