5yzk - Revision history

OCA at 10:34, 14 June 2023

OCA — Wed, 14 Jun 2023 10:34:15 GMT

←Older revision		Revision as of 10:34, 14 June 2023
Line 1:		Line 1:

	==Solution structure of LysM domain from a chitinase derived from Volvox carteri==		==Solution structure of LysM domain from a chitinase derived from Volvox carteri==
-	<StructureSection load='5yzk' size='340' side='right'caption='[[5yzk~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5yzk' size='340' side='right'caption='[[5yzk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5yzk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Volvox_carteri_f._nagariensis Volvox carteri f. nagariensis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5yzk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Volvox_carteri_f._nagariensis Volvox carteri f. nagariensis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZK 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;'>[[5yz6\|5yz6]]</div></td></tr>~~	+	</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=5yzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzk OCA], [https://pdbe.org/5yzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yzk RCSB], [https://www.ebi.ac.uk/pdbsum/5yzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzk ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">chi4, VOLCADRAFT_127242 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3068 Volvox carteri f. nagariensis])</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=5yzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzk OCA], [https://pdbe.org/5yzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yzk RCSB], [https://www.ebi.ac.uk/pdbsum/5yzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzk ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D8UFB5_VOLCA D8UFB5_VOLCA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Volvox carteri f. nagariensis]]		[[Category: Volvox carteri f. nagariensis]]
-	[[Category: Fukamizo, T]]	+	[[Category: Fukamizo T]]
-	[[Category: Kitaoku, Y]]	+	[[Category: Kitaoku Y]]
-	[[Category: Nishimura, S]]	+	[[Category: Nishimura S]]
-	[[Category: Ohnuma, T]]	+	[[Category: Ohnuma T]]
-	~~[[Category: Cbm50]]~~	+
-	~~[[Category: Chitin-specific]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lysin motif]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 09:50, 22 June 2022

OCA — Wed, 22 Jun 2022 09:50:16 GMT

←Older revision		Revision as of 09:50, 22 June 2022
Line 3:		Line 3:
	<StructureSection load='5yzk' size='340' side='right'caption='[[5yzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='5yzk' size='340' side='right'caption='[[5yzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YZK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Volvox_carteri_f._nagariensis Volvox carteri f. nagariensis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZK FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yz6\|5yz6]]</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;'>[[5yz6\|5yz6]]</div></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=5yzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzk OCA], [~~http~~://pdbe.org/5yzk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yzk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yzk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzk ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">chi4, VOLCADRAFT_127242 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3068 Volvox carteri f. nagariensis])</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=5yzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzk OCA], [https://pdbe.org/5yzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yzk RCSB], [https://www.ebi.ac.uk/pdbsum/5yzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two N-terminal lysin motifs (LysMs) found in a chitinase from the green alga Volvox carteri (VcLysM1 and VcLysM2) were produced, and their structures and chitin-binding properties were characterized. The binding affinities of VcLysM1 toward chitin oligomers determined by isothermal titration calorimetry (ITC) were higher than those of VcLysM2 by 0.8-1.1 kcal/mol of DeltaG degrees . Based on the NMR solution structures of the two LysMs, the differences in binding affinities were found to result from amino acid substitutions at the binding site. The NMR spectrum of a two-domain protein (VcLysM1+2), in which VcLysM1 and VcLysM2 are linked in tandem through a flexible linker, suggested that the individual domains of VcLysM1+2 independently fold and do not interact with each other. ITC analysis of chitin-oligomer binding revealed two different binding sites in VcLysM1+2, showing no cooperativity. The binding affinities of the VcLysM1 domain in VcLysM1+2 were lower than those of VcLysM1 alone, probably due to the flexible linker destabilizing the interaction between the chito-oligosaccahrides and VcLysM1 domain. Overall, two LysMs attached to the chitinase from the primitive plant species, V. carteri, were found to resemble bacterial LysMs reported thus far.
		+
		+	Structures and chitin-binding properties of two N-terminal lysin motifs (LysMs) found in a chitinase from Volvox carteri.,Kitaoku Y, Nishimura S, Hirono T, Suginta W, Ohnuma T, Fukamizo T Glycobiology. 2019 Jul 1;29(7):565-575. doi: 10.1093/glycob/cwz024. PMID:30976779<ref>PMID:30976779</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yzk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Volvox carteri f. nagariensis]]
	[[Category: Fukamizo, T]]		[[Category: Fukamizo, T]]
	[[Category: Kitaoku, Y]]		[[Category: Kitaoku, Y]]

OCA at 09:32, 21 October 2020

OCA — Wed, 21 Oct 2020 09:32:06 GMT

←Older revision		Revision as of 09:32, 21 October 2020
Line 1:		Line 1:

	==Solution structure of LysM domain from a chitinase derived from Volvox carteri==		==Solution structure of LysM domain from a chitinase derived from Volvox carteri==
-	<StructureSection load='5yzk' size='340' side='right' caption='[[5yzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5yzk' size='340' side='right'caption='[[5yzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YZK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YZK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yz6\|5yz6]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yz6\|5yz6]]</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=5yzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzk OCA], [http://pdbe.org/5yzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzk RCSB], [http://www.ebi.ac.uk/pdbsum/5yzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzk ProSAT]</span></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=5yzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzk OCA], [http://pdbe.org/5yzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzk RCSB], [http://www.ebi.ac.uk/pdbsum/5yzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzk ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fukamizo, T]]		[[Category: Fukamizo, T]]
	[[Category: Kitaoku, Y]]		[[Category: Kitaoku, Y]]

OCA at 08:10, 19 December 2018

OCA — Wed, 19 Dec 2018 08:10:06 GMT

←Older revision		Revision as of 08:10, 19 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5yzk is ON HOLD until Paper Publication~~	+	==Solution structure of LysM domain from a chitinase derived from Volvox carteri==
-		+	<StructureSection load='5yzk' size='340' side='right' caption='[[5yzk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors: Kitaoku, Y., Nishimura, S., Fukamizo, T., Ohnuma, T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yzk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZK FirstGlance]. <br>
-	~~Description:~~ Solution structure of LysM domain from a chitinase derived from Volvox carteri	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yz6\|5yz6]]</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=5yzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzk OCA], [http://pdbe.org/5yzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzk RCSB], [http://www.ebi.ac.uk/pdbsum/5yzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzk ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fukamizo, T]]		[[Category: Fukamizo, T]]
	[[Category: Kitaoku, Y]]		[[Category: Kitaoku, Y]]
		+	[[Category: Nishimura, S]]
	[[Category: Ohnuma, T]]		[[Category: Ohnuma, T]]
-	[[Category: ~~Nishimura, S~~]]	+	[[Category: Cbm50]]
		+	[[Category: Chitin-specific]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lysin motif]]
		+	[[Category: Sugar binding protein]]

OCA at 04:56, 7 February 2018

OCA — Wed, 07 Feb 2018 04:56:55 GMT

←Older revision		Revision as of 04:56, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yzk is ON HOLD	+	The entry 5yzk is ON HOLD until Paper Publication

	Authors: Kitaoku, Y., Nishimura, S., Fukamizo, T., Ohnuma, T.		Authors: Kitaoku, Y., Nishimura, S., Fukamizo, T., Ohnuma, T.

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

OCA — Wed, 20 Dec 2017 04:53:56 GMT

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

←Older revision

Revision as of 04:53, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yzk is ON HOLD Authors: Kitaoku, Y., Nishimura, S., Fukamizo, T., Ohnuma, T. Description: Solution structure of LysM domain from a chitinase deriv...

OCA — Wed, 20 Dec 2017 04:53:55 GMT

New page: '''Unreleased structure''' The entry 5yzk is ON HOLD Authors: Kitaoku, Y., Nishimura, S., Fukamizo, T., Ohnuma, T. Description: Solution structure of LysM domain from a chitinase deriv...

New page

'''Unreleased structure'''

The entry 5yzk is ON HOLD

Authors: Kitaoku, Y., Nishimura, S., Fukamizo, T., Ohnuma, T.

Description: Solution structure of LysM domain from a chitinase derived from Volvox carteri
[[Category: Unreleased Structures]]
[[Category: Fukamizo, T]]
[[Category: Kitaoku, Y]]
[[Category: Ohnuma, T]]
[[Category: Nishimura, S]]