3bll - Revision history

OCA at 14:47, 1 November 2023

2023-11-01T14:47:59Z

←Older revision		Revision as of 14:47, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3bll' size='340' side='right'caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>		<StructureSection load='3bll' size='340' side='right'caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bll]] is a 1 chain structure with sequence from [https://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=3BLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bll]] 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=3BLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPQ:TERT-BUTYL+[(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL]CARBAMATE'>BPQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.26Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nso\|2nso]], [[2nqz\|2nqz]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPQ:TERT-BUTYL+[(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL]CARBAMATE'>BPQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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 ([https://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'>[https://en.wikipedia.org/wiki/tRNA-guanine(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [https://pdbe.org/3bll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [https://www.ebi.ac.uk/pdbsum/3bll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bll 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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [https://pdbe.org/3bll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [https://www.ebi.ac.uk/pdbsum/3bll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bll ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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]	+	[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]]
Line 33:		Line 31:

	==See Also==		==See Also==
-	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]	+	*[[TRNA-guanine transglycosylase 3D structures\|TRNA-guanine transglycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Heine, A]]	+	[[Category: Zymomonas mobilis]]
-	[[Category: Klebe, G]]	+	[[Category: Heine A]]
-	[[Category: Reuter, K]]	+	[[Category: Klebe G]]
-	[[Category: Tidten, N]]	+	[[Category: Reuter K]]
-	~~[[Category: Boc-preq1]]~~	+	[[Category: Tidten N]]
-	~~[[Category: Glycosyltransferase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Queuosine biosynthesis]]~~	+
-	~~[[Category: Tgt mutant]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trna processing~~]]	+

OCA at 07:27, 10 November 2021

2021-11-10T07:27:20Z

←Older revision		Revision as of 07:27, 10 November 2021
Line 1:		Line 1:

	==TGT mutant in complex with Boc-preQ1==		==TGT mutant in complex with Boc-preQ1==
-	<StructureSection load='3bll' size='340' side='right' caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>	+	<StructureSection load='3bll' size='340' side='right'caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bll]] 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=3BLL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BLL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bll]] is a 1 chain structure with sequence from [https://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=3BLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPQ:TERT-BUTYL+[(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL]CARBAMATE'>BPQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=BPQ:TERT-BUTYL+[(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL]CARBAMATE'>BPQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[2nso\|2nso]], [[2nqz\|2nqz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nso\|2nso]], [[2nqz\|2nqz]]</div></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 ([https://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'>[https://en.wikipedia.org/wiki/tRNA-guanine(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [https://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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [~~http~~://pdbe.org/3bll PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bll PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bll 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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [https://pdbe.org/3bll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [https://www.ebi.ac.uk/pdbsum/3bll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bll 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]]
Line 38:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Heine, A]]		[[Category: Heine, A]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]

OCA at 07:53, 31 October 2018

2018-10-31T07:53:10Z

←Older revision		Revision as of 07:53, 31 October 2018
Line 1:		Line 1:
		+
	==TGT mutant in complex with Boc-preQ1==		==TGT mutant in complex with Boc-preQ1==
	<StructureSection load='3bll' size='340' side='right' caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>		<StructureSection load='3bll' size='340' side='right' caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' 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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [http://pdbe.org/3bll PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [http://www.ebi.ac.uk/pdbsum/3bll 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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [http://pdbe.org/3bll PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [http://www.ebi.ac.uk/pdbsum/3bll PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bll 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/bl/3bll_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3bll_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 16:41, 8 February 2016

2016-02-08T16:41:27Z

←Older revision		Revision as of 16:41, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3bll' size='340' side='right' caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>		<StructureSection load='3bll' size='340' side='right' caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bll]] 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=3BLL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bll]] 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=3BLL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPQ:TERT-BUTYL+[(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL]CARBAMATE'>BPQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=BPQ:TERT-BUTYL+[(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL]CARBAMATE'>BPQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[2nso\|2nso]], [[2nqz\|2nqz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nso\|2nso]], [[2nqz\|2nqz]]</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(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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [http://www.ebi.ac.uk/pdbsum/3bll 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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [http://pdbe.org/3bll PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [http://www.ebi.ac.uk/pdbsum/3bll PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3bll ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3bll" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Zymomonas mobilis]]
	[[Category: Heine, A]]		[[Category: Heine, A]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]

OCA at 00:44, 25 December 2014

2014-12-25T00:44:22Z

←Older revision		Revision as of 00:44, 25 December 2014
Line 9:		Line 9:
	<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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [http://www.ebi.ac.uk/pdbsum/3bll 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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [http://www.ebi.ac.uk/pdbsum/3bll 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]]

OCA at 13:44, 18 December 2014

2014-12-18T13:44:44Z

←Older revision		Revision as of 13:44, 18 December 2014
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-	~~{{STRUCTURE_3bll~~\| ~~PDB~~=3bll \| ~~SCENE~~= }}	+	==TGT mutant in complex with Boc-preQ1==
-	===~~TGT mutant in complex~~ with ~~Boc~~-~~preQ1~~===	+	<StructureSection load='3bll' size='340' side='right' caption='[[3bll]], [[Resolution\|resolution]] 1.26Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23704982}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bll]] 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=3BLL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPQ:TERT-BUTYL+[(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL]CARBAMATE'>BPQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[2nso\|2nso]], [[2nqz\|2nqz]]</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='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=3bll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bll OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bll RCSB], [http://www.ebi.ac.uk/pdbsum/3bll 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/bl/3bll_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 ==
		+	Bacterial tRNA-guanine transglycosylase (Tgt) catalyses the exchange of the genetically encoded guanine at the wobble position of tRNAs(His,Tyr,Asp,Asn) by the premodified base preQ1, which is further converted to queuine at the tRNA level. As eucaryotes are not able to synthesise queuine de novo but acquire it through their diet, eucaryotic Tgt directly inserts the hypermodified base into the wobble position of the tRNAs mentioned above. Bacterial Tgt is required for the efficient pathogenicity of Shigella sp, the causative agent of bacillary dysentery and, hence, it constitutes a putative target for the rational design of anti-Shigellosis compounds. Since mammalian Tgt is known to be indirectly essential to the conversion of phenylalanine to tyrosine, it is necessary to create substances which only inhibit bacterial but not eucaryotic Tgt. Therefore, it seems of utmost importance to study selectivity-determining features within both types of proteins. Homology models of Caenorhabditis elegans Tgt and human Tgt suggest that the replacement of Cys158 and Val233 in bacterial Tgt (Zymomonas mobilis Tgt numbering) by valine and accordingly glycine in eucaryotic Tgt largely accounts for the different substrate specificities. In the present study we have created mutated variants of Z. mobilis Tgt in order to investigate the impact of a Cys158Val and a Val233Gly exchange on catalytic activity and substrate specificity. Using enzyme kinetics and X-ray crystallography, we gained evidence that the Cys158Val mutation reduces the affinity to preQ1 while leaving the affinity to guanine unaffected. The Val233Gly exchange leads to an enlarged substrate binding pocket, that is necessary to accommodate queuine in a conformation compatible with the intermediately covalently bound tRNA molecule. Contrary to our expectations, we found that a priori queuine is recognised by the binding pocket of bacterial Tgt without, however, being used as a substrate.

-	~~==Function==~~	+	Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor.,Biela I, Tidten-Luksch N, Immekus F, Glinca S, Nguyen TX, Gerber HD, Heine A, Klebe G, Reuter K PLoS One. 2013 May 21;8(5):e64240. doi: 10.1371/journal.pone.0064240. Print 2013. PMID:23704982<ref>PMID:23704982</ref>
-	~~[[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]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3bll]] 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=3BLL OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]		*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023704982</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Zymomonas mobilis]]		[[Category: Zymomonas mobilis]]
-	[[Category: Heine, A.]]	+	[[Category: Heine, A]]
-	[[Category: Klebe, G.]]	+	[[Category: Klebe, G]]
-	[[Category: Reuter, K.]]	+	[[Category: Reuter, K]]
-	[[Category: Tidten, N.]]	+	[[Category: Tidten, N]]
	[[Category: Boc-preq1]]		[[Category: Boc-preq1]]
	[[Category: Glycosyltransferase]]		[[Category: Glycosyltransferase]]

OCA at 04:36, 18 July 2013

2013-07-18T04:36:01Z

←Older revision		Revision as of 04:36, 18 July 2013
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-	[[Image:3bll.png\|left\|200px]]
-
	{{STRUCTURE_3bll\| PDB=3bll \| SCENE= }}		{{STRUCTURE_3bll\| PDB=3bll \| SCENE= }}
-
	===TGT mutant in complex with Boc-preQ1===		===TGT mutant in complex with Boc-preQ1===
		+	{{ABSTRACT_PUBMED_23704982}}

		+	==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]

	==About this Structure==		==About this Structure==
	[[3bll]] 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=3BLL OCA].		[[3bll]] 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=3BLL OCA].
		+
		+	==See Also==
		+	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023704982</ref><references group="xtra"/><references/>
	[[Category: Zymomonas mobilis]]		[[Category: Zymomonas mobilis]]
-	[[Category: TRNA-guanine transglycosylase]]
	[[Category: Heine, A.]]		[[Category: Heine, A.]]
	[[Category: Klebe, G.]]		[[Category: Klebe, G.]]

OCA: Protected "3bll" [edit=sysop:move=sysop]

2013-01-07T20:50:44Z

Protected "3bll" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:50, 7 January 2013

OCA at 20:50, 7 January 2013

2013-01-07T20:50:40Z

←Older revision		Revision as of 20:50, 7 January 2013
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-	~~{{Seed}}~~	+	[[Image:3bll.png\|left\|200px]]
-	[[Image:3bll.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bll", 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_3bll\| PDB=3bll \| SCENE= }}		{{STRUCTURE_3bll\| PDB=3bll \| SCENE= }}

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	==About this Structure==		==About this Structure==
-	~~3BLL~~ 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=3BLL OCA].	+	[[3bll]] 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=3BLL OCA].
-	~~[[Category: Queuine tRNA-ribosyltransferase]]~~	+
	[[Category: Zymomonas mobilis]]		[[Category: Zymomonas mobilis]]
		+	[[Category: TRNA-guanine transglycosylase]]
	[[Category: Heine, A.]]		[[Category: Heine, A.]]
	[[Category: Klebe, G.]]		[[Category: Klebe, G.]]
Line 28:		Line 21:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trna processing]]		[[Category: Trna processing]]
-	[[Category: Zinc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 17 13:40:01 2008''

OCA at 11:40, 17 December 2008

2008-12-17T11:40:04Z

←Older revision		Revision as of 11:40, 17 December 2008
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3bll.jpg\|left\|200px]]

-	The ~~entry 3bll~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3bll", 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_3bll\| PDB=3bll \| SCENE= }}

-	~~Authors: Tidten, N., Heine, A., Klebe, G., Reuter, K.~~	+	===TGT mutant in complex with Boc-preQ1===

-	Description: TGT mutant in complex with Boc-preQ1

		+	==About this Structure==
		+	3BLL 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=3BLL OCA].
		+	[[Category: Queuine tRNA-ribosyltransferase]]
		+	[[Category: Zymomonas mobilis]]
		+	[[Category: Heine, A.]]
		+	[[Category: Klebe, G.]]
		+	[[Category: Reuter, K.]]
		+	[[Category: Tidten, N.]]
		+	[[Category: Boc-preq1]]
		+	[[Category: Glycosyltransferase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Queuosine biosynthesis]]
		+	[[Category: Tgt mutant]]
		+	[[Category: Transferase]]
		+	[[Category: Trna processing]]
		+	[[Category: Zinc]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 11 09:26~~:40 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 17 13:40:01 2008''