4gcx - Revision history

OCA at 15:43, 14 March 2024

OCA — Thu, 14 Mar 2024 15:43:49 GMT

←Older revision		Revision as of 15:43, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4gcx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_ZM4_=_ATCC_31821 Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GCX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4gcx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_ZM4_=_ATCC_31821 Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GCX 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=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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]] 1.42Å</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=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4gcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcx OCA], [https://pdbe.org/4gcx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gcx RCSB], [https://www.ebi.ac.uk/pdbsum/4gcx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcx 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=4gcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcx OCA], [https://pdbe.org/4gcx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gcx RCSB], [https://www.ebi.ac.uk/pdbsum/4gcx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcx 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]
-	<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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4gcx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[TRNA-guanine transglycosylase 3D structures\|TRNA-guanine transglycosylase 3D structures]]		*[[TRNA-guanine transglycosylase 3D structures\|TRNA-guanine transglycosylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:48, 26 October 2022

OCA — Wed, 26 Oct 2022 06:48:27 GMT

←Older revision		Revision as of 06:48, 26 October 2022
Line 1:		Line 1:

	==tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1==		==tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1==
-	<StructureSection load='4gcx' size='340' side='right' caption='[[4gcx]], [[Resolution\|resolution]] 1.42Å' scene=''>	+	<StructureSection load='4gcx' size='340' side='right'caption='[[4gcx]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gcx]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Zymmo Zymmo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GCX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gcx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_ZM4_=_ATCC_31821 Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GCX 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=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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">[[3bl3\|3bl3]], [[3bld\|3bld]], [[3bll\|3bll]], [[3blo\|3blo]], [[2nso\|2nso]], [[2nqz\|2nqz]], [[4gd0\|4gd0]]</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=4gcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcx OCA], [https://pdbe.org/4gcx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gcx RCSB], [https://www.ebi.ac.uk/pdbsum/4gcx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcx ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264203 ZYMMO])</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=4gcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcx OCA], [~~http~~://pdbe.org/4gcx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gcx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gcx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcx 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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:

	==See Also==		==See Also==
-	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]	+	*[[TRNA-guanine transglycosylase 3D structures\|TRNA-guanine transglycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Zymmo~~]]	+	[[Category: Large Structures]]
-	[[Category: Heine, A]]	+	[[Category: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]]
-	[[Category: Klebe, G]]	+	[[Category: Heine A]]
-	[[Category: Reuter, K]]	+	[[Category: Klebe G]]
-	[[Category: Schmidt, I]]	+	[[Category: Reuter K]]
-	[[Category: Tidten-Luksch, N]]	+	[[Category: Schmidt I]]
-	~~[[Category: Bacterial tgt]]~~	+	[[Category: Tidten-Luksch N]]
-	~~[[Category: Guanine exchange enzyme]]~~	+
-	~~[[Category: Preq1]]~~	+
-	~~[[Category: Substrate specifity]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trna~~]]	+

OCA at 08:36, 4 August 2016

OCA — Thu, 04 Aug 2016 08:36:39 GMT

←Older revision		Revision as of 08:36, 4 August 2016
Line 1:		Line 1:
		+
	==tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1==		==tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1==
	<StructureSection load='4gcx' size='340' side='right' caption='[[4gcx]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='4gcx' size='340' side='right' caption='[[4gcx]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gcx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Zymomonas_mobilis_subsp._mobilis_zm4 Zymomonas mobilis subsp. mobilis zm4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GCX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gcx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymmo Zymmo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GCX 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=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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">[[3bl3\|3bl3]], [[3bld\|3bld]], [[3bll\|3bll]], [[3blo\|3blo]], [[2nso\|2nso]], [[2nqz\|2nqz]], [[4gd0\|4gd0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bl3\|3bl3]], [[3bld\|3bld]], [[3bll\|3bll]], [[3blo\|3blo]], [[2nso\|2nso]], [[2nqz\|2nqz]], [[4gd0\|4gd0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264203 ~~Zymomonas mobilis subsp. mobilis ZM4~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264203 ZYMMO])</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=4gcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gcx RCSB], [http://www.ebi.ac.uk/pdbsum/4gcx 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=4gcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcx OCA], [http://pdbe.org/4gcx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gcx RCSB], [http://www.ebi.ac.uk/pdbsum/4gcx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gcx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4gcx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Zymomonas mobilis subsp. mobilis zm4~~]]	+	[[Category: Zymmo]]
	[[Category: Heine, A]]		[[Category: Heine, A]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]

OCA at 07:46, 24 December 2014

OCA — Wed, 24 Dec 2014 07:46:16 GMT

←Older revision		Revision as of 07:46, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4gcx\| PDB=4gcx \| SCENE= }}~~	+	==tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1==
-	===tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1===	+	<StructureSection load='4gcx' size='340' side='right' caption='[[4gcx]], [[Resolution\|resolution]] 1.42Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23704982}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4gcx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_zm4 Zymomonas mobilis subsp. mobilis zm4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GCX FirstGlance]. <br>
-	==Function==	+	</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=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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">[[3bl3\|3bl3]], [[3bld\|3bld]], [[3bll\|3bll]], [[3blo\|3blo]], [[2nso\|2nso]], [[2nqz\|2nqz]], [[4gd0\|4gd0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264203 Zymomonas mobilis subsp. mobilis ZM4])</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=4gcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gcx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gcx RCSB], [http://www.ebi.ac.uk/pdbsum/4gcx PDBsum]</span></td></tr>
		+	</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]		[[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]
		+	<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.

-	~~==About this Structure==~~	+	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>
-	~~[[4gcx]] is a 1 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki~~/~~Zymomonas_mobilis_subsp~~.~~_mobilis_zm4 Zymomonas mobilis subsp~~. ~~mobilis zm4]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4GCX OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</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 subsp. mobilis zm4]]		[[Category: Zymomonas mobilis subsp. mobilis zm4]]
-	[[Category: Heine, A.]]	+	[[Category: Heine, A]]
-	[[Category: Klebe, G.]]	+	[[Category: Klebe, G]]
-	[[Category: Reuter, K.]]	+	[[Category: Reuter, K]]
-	[[Category: Schmidt, I.]]	+	[[Category: Schmidt, I]]
-	[[Category: Tidten-Luksch, N.]]	+	[[Category: Tidten-Luksch, N]]
	[[Category: Bacterial tgt]]		[[Category: Bacterial tgt]]
	[[Category: Guanine exchange enzyme]]		[[Category: Guanine exchange enzyme]]

OCA at 04:13, 18 July 2013

OCA — Thu, 18 Jul 2013 04:13:26 GMT

←Older revision		Revision as of 04:13, 18 July 2013
Line 1:		Line 1:
-	[[Image:4gcx.jpg\|left\|200px]]
-
	{{STRUCTURE_4gcx\| PDB=4gcx \| SCENE= }}		{{STRUCTURE_4gcx\| PDB=4gcx \| SCENE= }}
-
	===tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1===		===tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with 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==
-	[[4gcx]] 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=4GCX OCA].	+	[[4gcx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_zm4 Zymomonas mobilis subsp. mobilis zm4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GCX OCA].
-	[[~~Category: Zymomonas mobilis~~]]	+
-	[[Category: ~~TRNA-guanine transglycosylase~~]]	+	==See Also==
		+	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023704982</ref><references group="xtra"/><references/>
		+	[[Category: Zymomonas mobilis subsp. mobilis zm4]]
	[[Category: Heine, A.]]		[[Category: Heine, A.]]
	[[Category: Klebe, G.]]		[[Category: Klebe, G.]]

OCA at 05:30, 29 August 2012

OCA — Wed, 29 Aug 2012 05:30:13 GMT

←Older revision		Revision as of 05:30, 29 August 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4gcx.jpg\|left\|200px]]

-	~~The entry~~ 4gcx ~~is ON HOLD~~	+	{{STRUCTURE_4gcx\| PDB=4gcx \| SCENE= }}

-	~~Authors: Schmidt, I., Tidten~~-~~Luksch, N., Heine, A., Reuter, K.~~, ~~Klebe~~, G.	+	===tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1===

-	~~Description~~: ~~tRNA~~-guanine transglycosylase ~~Y106F~~, ~~C158V~~, ~~V233G mutant in complex with preQ1~~	+
		+	==About this Structure==
		+	[[4gcx]] 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=4GCX OCA].
		+	[[Category: Zymomonas mobilis]]
		+	[[Category: TRNA-guanine transglycosylase]]
		+	[[Category: Heine, A.]]
		+	[[Category: Klebe, G.]]
		+	[[Category: Reuter, K.]]
		+	[[Category: Schmidt, I.]]
		+	[[Category: Tidten-Luksch, N.]]
		+	[[Category: Bacterial tgt]]
		+	[[Category: Guanine exchange enzyme]]
		+	[[Category: Preq1]]
		+	[[Category: Substrate specifity]]
		+	[[Category: Transferase]]
		+	[[Category: Trna]]

OCA: Protected "4gcx" [edit=sysop:move=sysop]

OCA — Wed, 08 Aug 2012 05:00:46 GMT

Protected "4gcx" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:00, 8 August 2012

OCA: New page: '''Unreleased structure''' The entry 4gcx is ON HOLD Authors: Schmidt, I., Tidten-Luksch, N., Heine, A., Reuter, K., Klebe, G. Description: tRNA-guanine transglycosylase Y106F, C158V, ...

OCA — Wed, 08 Aug 2012 05:00:45 GMT

New page: '''Unreleased structure''' The entry 4gcx is ON HOLD Authors: Schmidt, I., Tidten-Luksch, N., Heine, A., Reuter, K., Klebe, G. Description: tRNA-guanine transglycosylase Y106F, C158V, ...

New page

'''Unreleased structure'''

The entry 4gcx is ON HOLD

Authors: Schmidt, I., Tidten-Luksch, N., Heine, A., Reuter, K., Klebe, G.

Description: tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1