5y0m - Revision history

OCA at 10:08, 15 November 2023

OCA — Wed, 15 Nov 2023 10:08:03 GMT

←Older revision		Revision as of 10:08, 15 November 2023
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	<StructureSection load='5y0m' size='340' side='right'caption='[[5y0m]], [[Resolution\|resolution]] 1.03Å' scene=''>		<StructureSection load='5y0m' size='340' side='right'caption='[[5y0m]], [[Resolution\|resolution]] 1.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0m]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Flavobacterium_sp.~~_ki723t1~~ Flavobacterium sp. ~~ki723t1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp._KI723T1 Flavobacterium sp. KI723T1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y0M 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=PO4:PHOSPHATE+ION'>PO4</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]] 1.03Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nylC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=408956 Flavobacterium sp. KI723T1])</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=PO4:PHOSPHATE+ION'>PO4</scene></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=5y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0m OCA], [~~http~~://pdbe.org/5y0m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y0m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y0m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0m 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=5y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0m OCA], [https://pdbe.org/5y0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y0m RCSB], [https://www.ebi.ac.uk/pdbsum/5y0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NYLC_FLASK NYLC_FLASK]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium sp. ~~ki723t1~~]]	+	[[Category: Flavobacterium sp. KI723T1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Higuchi, Y]]	+	[[Category: Higuchi Y]]
-	[[Category: Nagai, K]]	+	[[Category: Nagai K]]
-	[[Category: Negoro, S]]	+	[[Category: Negoro S]]
-	[[Category: Shibata, N]]	+	[[Category: Shibata N]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nylon oligomer~~]]	+

OCA at 07:02, 14 October 2020

OCA — Wed, 14 Oct 2020 07:02:43 GMT

←Older revision		Revision as of 07:02, 14 October 2020
Line 1:		Line 1:

	==Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q muntant==		==Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q muntant==
-	<StructureSection load='5y0m' size='340' side='right' caption='[[5y0m]], [[Resolution\|resolution]] 1.03Å' scene=''>	+	<StructureSection load='5y0m' size='340' side='right'caption='[[5y0m]], [[Resolution\|resolution]] 1.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0M OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp._ki723t1 Flavobacterium sp. ki723t1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y0M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=PO4:PHOSPHATE+ION'>PO4</scene></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=5y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0m OCA], [http://pdbe.org/5y0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0m RCSB], [http://www.ebi.ac.uk/pdbsum/5y0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0m ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nylC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=408956 Flavobacterium sp. KI723T1])</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=5y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0m OCA], [http://pdbe.org/5y0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0m RCSB], [http://www.ebi.ac.uk/pdbsum/5y0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0m ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nylon hydrolase (NylC) is initially expressed as an inactive precursor (36 kDa). The precursor is cleaved autocatalytically at Asn266/Thr267 to generate an active enzyme composed of an alpha subunit (27 kDa) and a beta subunit (9 kDa). Four alphabeta heterodimers (molecules A-D) form a doughnut-shaped quaternary structure. In this study, the thermostability of the parental NylC was altered by amino acid substitutions located at the A/D interface (D122G/H130Y/D36A/L137A) or the A/B interface (E263Q) and spanned a range of 47 degrees C. Considering structural, biophysical, and biochemical analyses, we discuss the structural basis of the stability of nylon hydrolase. From the analytical centrifugation data obtained regarding the various mutant enzymes, we conclude that the assembly of the monomeric units is dynamically altered by the mutations. Finally, we propose a model that can predict whether the fate of the nascent polypeptide will be correct subunit assembly, inappropriate protein-protein interactions causing aggregation, or intracellular degradation of the polypeptide.
		+
		+	Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase.,Negoro S, Shibata N, Lee YH, Takehara I, Kinugasa R, Nagai K, Tanaka Y, Kato DI, Takeo M, Goto Y, Higuchi Y Sci Rep. 2018 Jun 27;8(1):9725. doi: 10.1038/s41598-018-27860-w. PMID:29950566<ref>PMID:29950566</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y0m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium sp. ki723t1]]
		+	[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Nagai, K]]		[[Category: Nagai, K]]

OCA at 07:09, 25 July 2018

OCA — Wed, 25 Jul 2018 07:09:41 GMT

←Older revision		Revision as of 07:09, 25 July 2018
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-	'''Unreleased structure'''

-	~~The entry 5y0m is ON HOLD until Paper Publication~~	+	==Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q muntant==
-		+	<StructureSection load='5y0m' size='340' side='right' caption='[[5y0m]], [[Resolution\|resolution]] 1.03Å' scene=''>
-	~~Authors: Negoro, S., Shibata, N., Nagai, K., Higuchi, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y0m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0M FirstGlance]. <br>
-	~~Description:~~ Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q muntant	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0m OCA], [http://pdbe.org/5y0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0m RCSB], [http://www.ebi.ac.uk/pdbsum/5y0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0m ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Negoro~~, S]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Nagai, K]]		[[Category: Nagai, K]]
		+	[[Category: Negoro, S]]
	[[Category: Shibata, N]]		[[Category: Shibata, N]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nylon oligomer]]

OCA: Protected "5y0m" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:00:10 GMT

Protected "5y0m" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:00, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y0m is ON HOLD until Paper Publication Authors: Negoro, S., Shibata, N., Nagai, K., Higuchi, Y. Description: Structure of 6-aminohexanoate-oligome...

OCA — Wed, 27 Sep 2017 16:00:09 GMT

New page: '''Unreleased structure''' The entry 5y0m is ON HOLD until Paper Publication Authors: Negoro, S., Shibata, N., Nagai, K., Higuchi, Y. Description: Structure of 6-aminohexanoate-oligome...

New page

'''Unreleased structure'''

The entry 5y0m is ON HOLD until Paper Publication

Authors: Negoro, S., Shibata, N., Nagai, K., Higuchi, Y.

Description: Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q muntant
[[Category: Unreleased Structures]]
[[Category: Negoro, S]]
[[Category: Higuchi, Y]]
[[Category: Nagai, K]]
[[Category: Shibata, N]]