6xk1 - Revision history

OCA at 14:53, 18 October 2023

OCA — Wed, 18 Oct 2023 14:53:57 GMT

←Older revision		Revision as of 14:53, 18 October 2023
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	<StructureSection load='6xk1' size='340' side='right'caption='[[6xk1]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6xk1' size='340' side='right'caption='[[6xk1]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xk1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp.~~_mel~~ Rhodococcus sp. ~~mel~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xk1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp._Mel Rhodococcus sp. Mel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XK1 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[6xix\|6xix]], [[6xj4\|6xj4]], [[6xje\|6xje]], [[6xjm\|6xjm]]</div></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]] 1.7Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">biuH ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1093626 Rhodococcus sp. Mel])~~</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=6xk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xk1 OCA], [https://pdbe.org/6xk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xk1 RCSB], [https://www.ebi.ac.uk/pdbsum/6xk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xk1 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=6xk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xk1 OCA], [https://pdbe.org/6xk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xk1 RCSB], [https://www.ebi.ac.uk/pdbsum/6xk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xk1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/H8ZKV9_9NOCA H8ZKV9_9NOCA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rhodococcus sp. ~~mel~~]]	+	[[Category: Rhodococcus sp. Mel]]
-	[[Category: Elias~~, M H~~]]	+	[[Category: Elias MH]]
-	[[Category: Tassoulas~~, L T~~]]	+	[[Category: Tassoulas LT]]
-	[[Category: Wackett~~, L P]]~~	+	[[Category: Wackett LP]]
-	~~[[Category: Biuh]]~~	+
-	~~[[Category: Biuret]]~~	+
-	~~[[Category: Cysteine hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nitrogen]]~~	+
-	~~[[Category: Triuret]]~~	+
-	~~[[Category: Trta~~]]	+

OCA at 10:01, 14 July 2021

OCA — Wed, 14 Jul 2021 10:01:18 GMT

←Older revision		Revision as of 10:01, 14 July 2021
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	==Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form==		==Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form==
-	<StructureSection load='6xk1' size='340' side='right'caption='[[6xk1]]' scene=''>	+	<StructureSection load='6xk1' size='340' side='right'caption='[[6xk1]], [[Resolution\|resolution]] 1.70Å' 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=6XK1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6XK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xk1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp._mel Rhodococcus sp. mel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XK1 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=6xk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xk1 OCA], [~~http~~://pdbe.org/6xk1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6xk1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6xk1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6xk1 ProSAT]</span></td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6xix\|6xix]], [[6xj4\|6xj4]], [[6xje\|6xje]], [[6xjm\|6xjm]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">biuH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1093626 Rhodococcus sp. Mel])</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=6xk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xk1 OCA], [https://pdbe.org/6xk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xk1 RCSB], [https://www.ebi.ac.uk/pdbsum/6xk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xk1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Triuret (carbonyldiurea) is an impurity found in industrial urea fertilizer (<0.1% w/w) that is applied, worldwide, around 300 million pounds each year on agricultural lands. In addition to anthropogenic sources, endogenous triuret has been identified in amoeba and human urine, the latter being diagnostic for hypokalemia. The present study is the first to describe the metabolic breakdown of triuret, which funnels into biuret metabolism. We identified the gene responsible for triuret decomposition (trtA) in bacterial genomes, clustered with biuH, that encodes biuret hydrolase and has close protein sequence homology. TrtA is a member of the isochorismatase-like hydrolase protein family (IHL), similarly to BiuH, and has a catalytic efficiency (kcat/KM) of 6 x 10(5) (M(-1)s(-1)), a KM for triuret of 20 muM, and exquisite substrate specificity. Indeed, TrtA has four orders of magnitude less activity with biuret. Crystal structures of TrtA in apo and holo form were solved and compared to the BiuH structure. The high substrate selectivity was found to be conveyed by second shell residues around each active site. Mutagenesis of residues conserved in TrtA to the alternate consensus found in BiuHs revealed residues critical to triuret hydrolase activity but no single mutant evolved more biuret activity and likely a combination of mutations is required to interconvert between TrtA, BiuH functions. TrtA-mediated triuret metabolism is relatively rare in recorded genomes (1-2%), but is largely found in plant-associated, nodulating and endophytic bacteria. This study suggests functions for triuret hydrolase in certain eukaryotic intermediary processes and prokaryotic intermediary or biodegradative metabolism.
		+
		+	Discovery of an ultra-specific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway.,Tassoulas LJ, Elias MH, Wackett LP J Biol Chem. 2020 Nov 10. pii: RA120.015631. doi: 10.1074/jbc.RA120.015631. PMID:33172891<ref>PMID:33172891</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xk1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Elias MH]]	+	[[Category: Rhodococcus sp. mel]]
-	[[Category: Tassoulas LT]]	+	[[Category: Elias, M H]]
-	[[Category: Wackett LP]]	+	[[Category: Tassoulas, L T]]
		+	[[Category: Wackett, L P]]
		+	[[Category: Biuh]]
		+	[[Category: Biuret]]
		+	[[Category: Cysteine hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nitrogen]]
		+	[[Category: Triuret]]
		+	[[Category: Trta]]

OCA at 09:37, 18 November 2020

OCA — Wed, 18 Nov 2020 09:37:54 GMT

←Older revision		Revision as of 09:37, 18 November 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6xk1 ~~is ON HOLD until Paper Publication~~	+	==Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form==
-		+	<StructureSection load='6xk1' size='340' side='right'caption='[[6xk1]]' scene=''>
-	~~Authors~~: ~~Tassoulas~~, L.T., ~~Elias~~, M.H., ~~Wackett~~, L.P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XK1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XK1 FirstGlance]. <br>
-	~~Description: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form~~	+	</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=6xk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xk1 OCA], [http://pdbe.org/6xk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6xk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xk1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Tassoulas, L.T~~]]	+	__TOC__
-	[[Category: ~~Wackett, L.P~~]]	+	</StructureSection>
-	[[Category: ~~Elias, M.H~~]]	+	[[Category: Large Structures]]
		+	[[Category: Elias MH]]
		+	[[Category: Tassoulas LT]]
		+	[[Category: Wackett LP]]

OCA at 06:42, 22 July 2020

OCA — Wed, 22 Jul 2020 06:42:44 GMT

←Older revision		Revision as of 06:42, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xk1 is ON HOLD	+	The entry 6xk1 is ON HOLD until Paper Publication

	Authors: Tassoulas, L.T., Elias, M.H., Wackett, L.P.		Authors: Tassoulas, L.T., Elias, M.H., Wackett, L.P.

-	Description: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S ~~co-crystallized with triuret~~	+	Description: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Tassoulas, L.T]]		[[Category: Tassoulas, L.T]]
	[[Category: Wackett, L.P]]		[[Category: Wackett, L.P]]
	[[Category: Elias, M.H]]		[[Category: Elias, M.H]]

OCA: Protected "6xk1" [edit=sysop:move=sysop]

OCA — Wed, 08 Jul 2020 10:53:19 GMT

Protected "6xk1" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:53, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6xk1 is ON HOLD Authors: Tassoulas, L.T., Elias, M.H., Wackett, L.P. Description: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S co-crystal...

OCA — Wed, 08 Jul 2020 10:53:18 GMT

New page: '''Unreleased structure''' The entry 6xk1 is ON HOLD Authors: Tassoulas, L.T., Elias, M.H., Wackett, L.P. Description: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S co-crystal...

New page

'''Unreleased structure'''

The entry 6xk1 is ON HOLD

Authors: Tassoulas, L.T., Elias, M.H., Wackett, L.P.

Description: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S co-crystallized with triuret
[[Category: Unreleased Structures]]
[[Category: Tassoulas, L.T]]
[[Category: Wackett, L.P]]
[[Category: Elias, M.H]]