5utj - Revision history

OCA at 10:10, 18 March 2020

OCA — Wed, 18 Mar 2020 10:10:45 GMT

←Older revision		Revision as of 10:10, 18 March 2020
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	== 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]		[[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 ==
		+	Crystallography provides structural information crucial for fragment optimization, however several criteria must be met to screen directly on protein crystals as soakable, well-diffracting specimen must be available. We screened a 96-fragment library against the tRNA-modifying enzyme TGT using crystallography. Eight hits, some with surprising binding poses, were detected. However, the amount of data collection, reduction and refinement is assumed substantial. Therefore, having a reliable cascade of fast and cost-efficient methods available for pre-screening before embarking to elaborate crystallographic screening appears beneficial. This allows filtering of compounds to the most promising hits, available to rapidly progress from hit-to-lead. But how to ensure that this workflow is reliable? To answer this question, we also applied SPR and NMR to the same screening sample to study whether identical hits are retrieved. Upon hit-list comparisons, crystallography shows with NMR and SPR, only one overlapping hit and all three methods shared no common hits. This questions a cascade-type screening protocol at least in the current example. Compared to crystallography, SPR and NMR detected higher percentages of non-active-site binders suggesting the importance of running reporter ligand-based competitive screens in SPR and NMR, a requirement not needed in crystallography. Although not specific, NMR proved a more sensitive method relative to SPR and crystallography, as it picked up the highest numbers of binders.
		+
		+	Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies.,Hassaan E, Eriksson PO, Geschwindner S, Heine A, Klebe G ChemMedChem. 2020 Feb 5;15(3):324-337. doi: 10.1002/cmdc.201900604. Epub 2020 Jan, 29. PMID:31808981<ref>PMID:31808981</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5utj" style="background-color:#fffaf0;"></div>

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

OCA at 07:19, 26 June 2019

OCA — Wed, 26 Jun 2019 07:19:17 GMT

←Older revision		Revision as of 07:19, 26 June 2019
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	==Crystal Structure of TGT in complex with 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine==		==Crystal Structure of TGT in complex with 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine==
-	<StructureSection load='5utj' size='340' side='right' caption='[[5utj]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5utj' size='340' side='right'caption='[[5utj]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5utj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UTJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5utj]] 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=5UTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UTJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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, 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=5utj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utj OCA], [http://pdbe.org/5utj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5utj RCSB], [http://www.ebi.ac.uk/pdbsum/5utj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5utj ProSAT]</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=5utj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utj OCA], [http://pdbe.org/5utj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5utj RCSB], [http://www.ebi.ac.uk/pdbsum/5utj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5utj ProSAT]</span></td></tr>
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	== 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]		[[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]
		+
		+	==See Also==
		+	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Zymmo]]
	[[Category: Hassaan, E]]		[[Category: Hassaan, E]]
	[[Category: Heine, A]]		[[Category: Heine, A]]

OCA at 05:00, 8 March 2018

OCA — Thu, 08 Mar 2018 05:00:38 GMT

←Older revision		Revision as of 05:00, 8 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5utj is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of TGT in complex with 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine==
-		+	<StructureSection load='5utj' size='340' side='right' caption='[[5utj]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5utj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UTJ FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5utj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5utj OCA], [http://pdbe.org/5utj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5utj RCSB], [http://www.ebi.ac.uk/pdbsum/5utj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5utj ProSAT]</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]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hassaan, E]]
		+	[[Category: Heine, A]]
		+	[[Category: Klebe, G]]
		+	[[Category: Fragment]]
		+	[[Category: Guanine exchange enzyme]]
		+	[[Category: Tgt]]
		+	[[Category: Transferase]]
		+	[[Category: Transglycosylase]]
		+	[[Category: Trna]]

OCA: Protected "5utj" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 14:54:36 GMT

Protected "5utj" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:54, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5utj is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Mar 2017 14:54:34 GMT

New page: '''Unreleased structure''' The entry 5utj is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5utj is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]