5vnp - Revision history

OCA at 13:52, 4 October 2023

OCA — Wed, 04 Oct 2023 13:52:30 GMT

←Older revision		Revision as of 13:52, 4 October 2023
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	==X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand==		==X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand==
-	<StructureSection load='5vnp' size='340' side='right' caption='[[5vnp]], [[Resolution\|resolution]] 2.23Å' scene=''>	+	<StructureSection load='5vnp' size='340' side='right'caption='[[5vnp]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vnp]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacterium_mycoides_roseum"_grotenfelt_1889 "bacterium mycoides roseum" grotenfelt 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VNP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vnp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_rhodochrous Rhodococcus rhodochrous]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VNP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9FM:N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide'>9FM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.23Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1829 "Bacterium mycoides roseum" Grotenfelt 1889])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9FM:N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide'>9FM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] </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=5vnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnp OCA], [https://pdbe.org/5vnp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vnp RCSB], [https://www.ebi.ac.uk/pdbsum/5vnp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnp 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=5vnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnp OCA], [~~http~~://pdbe.org/5vnp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vnp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vnp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnp ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DHAA_RHORH DHAA_RHORH]] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Expresses halogenase activity against 1-chloroalkanes of chain length C3 to C10, and also shows a very weak activity with 1,2-dichloroethane.	+	[https://www.uniprot.org/uniprot/DHAA_RHORH DHAA_RHORH] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Expresses halogenase activity against 1-chloroalkanes of chain length C3 to C10, and also shows a very weak activity with 1,2-dichloroethane.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5vnp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vnp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium mycoides roseum grotenfelt 1889~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Haloalkane dehalogenase~~]]	+	[[Category: Rhodococcus rhodochrous]]
-	[[Category: Boal~~, A K~~]]	+	[[Category: Boal AK]]
-	[[Category: Dunham~~, N P]]~~	+	[[Category: Dunham NP]]
-	~~[[Category: Biosensor]]~~	+
-	~~[[Category: Cytotoxicity]]~~	+
-	~~[[Category: Fluorescent probe]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein aggregation]]~~	+
-	~~[[Category: Proteome stress~~]]	+

OCA at 06:14, 16 November 2017

OCA — Thu, 16 Nov 2017 06:14:11 GMT

←Older revision		Revision as of 06:14, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vnp is ~~ON HOLD~~	+	==X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand==
		+	<StructureSection load='5vnp' size='340' side='right' caption='[[5vnp]], [[Resolution\|resolution]] 2.23Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vnp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_mycoides_roseum"_grotenfelt_1889 "bacterium mycoides roseum" grotenfelt 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VNP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VNP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9FM:N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide'>9FM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1829 "Bacterium mycoides roseum" Grotenfelt 1889])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] </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=5vnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vnp OCA], [http://pdbe.org/5vnp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vnp RCSB], [http://www.ebi.ac.uk/pdbsum/5vnp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vnp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DHAA_RHORH DHAA_RHORH]] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Expresses halogenase activity against 1-chloroalkanes of chain length C3 to C10, and also shows a very weak activity with 1,2-dichloroethane.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Drug-induced proteome stress that involves protein aggregation may cause adverse effects and undermine the safety profile of a drug. Safety of drugs is regularly evaluated using cytotoxicity assays that measure cell death. However, these assays provide limited insights into the presence of proteome stress in live cells. A fluorogenic protein sensor is reported to detect drug-induced proteome stress prior to cell death. An aggregation prone Halo-tag mutant (AgHalo) was evolved to sense proteome stress through its aggregation. Detection of such conformational changes was enabled by a fluorogenic ligand that fluoresces upon AgHalo forming soluble aggregates. Using 5 common anticancer drugs, we exemplified detection of differential proteome stress before any cell death was observed. Thus, this sensor can be used to evaluate drug safety in a regime that the current cytotoxicity assays cannot cover and be generally applied to detect proteome stress induced by other toxins.

-	~~Authors~~: Dunham, ~~N.P.~~, Boal, A.K.	+	AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress.,Liu Y, Fares M, Dunham NP, Gao Z, Miao K, Jiang X, Bollinger SS, Boal AK, Zhang X Angew Chem Int Ed Engl. 2017 Jul 17;56(30):8672-8676. doi:, 10.1002/anie.201702417. Epub 2017 Jun 19. PMID:28557281<ref>PMID:28557281</ref>

-	~~Description: X-ray crystal structure~~ of ~~Halotag bound to~~ the ~~P1 benzoxadiazole fluorogenic ligand~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Dunham, N.P~~]]	+	<div class="pdbe-citations 5vnp" style="background-color:#fffaf0;"></div>
-	[[Category: Boal, A.K]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacterium mycoides roseum grotenfelt 1889]]
		+	[[Category: Haloalkane dehalogenase]]
		+	[[Category: Boal, A K]]
		+	[[Category: Dunham, N P]]
		+	[[Category: Biosensor]]
		+	[[Category: Cytotoxicity]]
		+	[[Category: Fluorescent probe]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein aggregation]]
		+	[[Category: Proteome stress]]

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

OCA — Wed, 10 May 2017 11:13:44 GMT

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

←Older revision

Revision as of 11:13, 10 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vnp is ON HOLD Authors: Dunham, N.P., Boal, A.K. Description: X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand...

OCA — Wed, 10 May 2017 11:13:43 GMT

New page: '''Unreleased structure''' The entry 5vnp is ON HOLD Authors: Dunham, N.P., Boal, A.K. Description: X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand...

New page

'''Unreleased structure'''

The entry 5vnp is ON HOLD

Authors: Dunham, N.P., Boal, A.K.

Description: X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand
[[Category: Unreleased Structures]]
[[Category: Dunham, N.P]]
[[Category: Boal, A.K]]