7apm - Revision history

OCA at 12:13, 1 February 2024

2024-02-01T12:13:42Z

←Older revision		Revision as of 12:13, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7apm' size='340' side='right'caption='[[7apm]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='7apm' size='340' side='right'caption='[[7apm]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7apm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Zymmo Zymmo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7apm]] 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=7APM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.66Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</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"><div style='overflow: auto; max-height: 3em;'>[[7apl\|7apl]]</div></td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt~~, ~~ZMO0363 ([https://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~~'>~~[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=7apm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apm OCA], [https://pdbe.org/7apm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apm RCSB], [https://www.ebi.ac.uk/pdbsum/7apm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apm 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=7apm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apm OCA], [https://pdbe.org/7apm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apm RCSB], [https://www.ebi.ac.uk/pdbsum/7apm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apm 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 21:

	==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 30:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Zymmo~~]]	+	[[Category: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]]
-	[[Category: Heine, A]]	+	[[Category: Heine A]]
-	[[Category: Klebe, G]]	+	[[Category: Klebe G]]
-	[[Category: Nguyen, D]]	+	[[Category: Nguyen D]]
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Spin label]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 20:13, 20 October 2021

2021-10-20T20:13:06Z

←Older revision		Revision as of 20:13, 20 October 2021
Line 1:		Line 1:

-	==tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL==	+	==tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL.==
	<StructureSection load='7apm' size='340' side='right'caption='[[7apm]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='7apm' size='340' side='right'caption='[[7apm]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 05:49, 6 October 2021

2021-10-06T05:49:43Z

←Older revision		Revision as of 05:49, 6 October 2021
Line 1:		Line 1:

	==tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL==		==tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL==
-	<StructureSection load='7apm' size='340' side='right'caption='[[7apm]]' scene=''>	+	<StructureSection load='7apm' size='340' side='right'caption='[[7apm]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7APM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7apm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymmo Zymmo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APM FirstGlance]. <br>
-	</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=7apm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apm OCA], [~~http~~://pdbe.org/7apm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7apm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7apm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7apm ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7apl\|7apl]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([https://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'>[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=7apm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apm OCA], [https://pdbe.org/7apm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apm RCSB], [https://www.ebi.ac.uk/pdbsum/7apm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apm ProSAT]</span></td></tr>
	</table>		</table>
		+	== 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]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mechanistic insights into protein-ligand interactions can yield chemical tools for modulating protein function and enable their use for therapeutic purposes. For the homodimeric enzyme tRNA-guanine transglycosylase (TGT), a putative virulence target of shigellosis, ligand binding has been shown by crystallography to transform the functional dimer geometry into an incompetent twisted one. However, crystallographic observation of both end states does neither verify the ligand-induced transformation of one dimer into the other in solution nor does it shed light on the underlying transformation mechanism. We addressed these questions in an approach that combines site-directed spin labeling (SDSL) with distance measurements based on pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy. We observed an equilibrium between the functional and twisted dimer that depends on the type of ligand, with a pyranose-substituted ligand being the most potent one in shifting the equilibrium toward the twisted dimer. Our experiments suggest a dissociation-association mechanism for the formation of the twisted dimer upon ligand binding.
		+
		+	Unraveling a Ligand-Induced Twist of a Homodimeric Enzyme by Pulsed Electron-Electron Double Resonance.,Nguyen D, Abdullin D, Heubach CA, Pfaffeneder T, Nguyen A, Heine A, Reuter K, Diederich F, Schiemann O, Klebe G Angew Chem Int Ed Engl. 2021 Aug 12. doi: 10.1002/anie.202108179. PMID:34387025<ref>PMID:34387025</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7apm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA-guanine transglycosylase\|TRNA-guanine transglycosylase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Heine A]]	+	[[Category: Zymmo]]
-	[[Category: Klebe G]]	+	[[Category: Heine, A]]
-	[[Category: Nguyen D]]	+	[[Category: Klebe, G]]
		+	[[Category: Nguyen, D]]
		+	[[Category: Enzyme]]
		+	[[Category: Spin label]]
		+	[[Category: Transferase]]

OCA: Protected "7apm" [edit=sysop:move=sysop]

2020-10-28T20:37:32Z

Protected "7apm" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:37, 28 October 2020

OCA: New page: ==tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL== == Structural highlights == ...
2020-10-28T20:37:30Z
New page: ==tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL== <StructureSection load='7apm' size='340' side='right'caption='7apm' scene=''> == Structural highlights == <table>...
New page

==tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL==
<StructureSection load='7apm' size='340' side='right'caption='[[7apm]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7APM FirstGlance]. <br>
</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=7apm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apm OCA], [http://pdbe.org/7apm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7apm RCSB], [http://www.ebi.ac.uk/pdbsum/7apm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7apm ProSAT]</span></td></tr>
</table>
TOC
</StructureSection>
[[Category: Large Structures]]
[[Category: Heine A]]
[[Category: Klebe G]]
[[Category: Nguyen D]]