6jhj - Revision history

OCA at 10:09, 22 November 2023

OCA — Wed, 22 Nov 2023 10:09:34 GMT

←Older revision		Revision as of 10:09, 22 November 2023
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	<StructureSection load='6jhj' size='340' side='right'caption='[[6jhj]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='6jhj' size='340' side='right'caption='[[6jhj]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jhj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aquimarina Aquimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JHJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jhj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquimarina Aquimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JHJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.69Å</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=6jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhj OCA], [~~http~~://pdbe.org/6jhj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jhj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jhj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhj ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=6jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhj OCA], [https://pdbe.org/6jhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jhj RCSB], [https://www.ebi.ac.uk/pdbsum/6jhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 6jhj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jhj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Laminarase 3D structures\|Laminarase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Aquimarina]]		[[Category: Aquimarina]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Long, L]]	+	[[Category: Long L]]
-	[[Category: Miyakawa, T]]	+	[[Category: Miyakawa T]]
-	[[Category: Tanokura, M]]	+	[[Category: Tanokura M]]
-	[[Category: Xu, Y]]	+	[[Category: Xu Y]]
-	[[Category: Yang, J]]	+	[[Category: Yang J]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:28, 7 October 2020

OCA — Wed, 07 Oct 2020 06:28:12 GMT

←Older revision		Revision as of 06:28, 7 October 2020
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhj OCA], [http://pdbe.org/6jhj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhj RCSB], [http://www.ebi.ac.uk/pdbsum/6jhj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhj 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=6jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhj OCA], [http://pdbe.org/6jhj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhj RCSB], [http://www.ebi.ac.uk/pdbsum/6jhj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Laminarin is an abundant algal polysaccharide that serves as carbon storage and fuel to meet the nutrition demands of heterotrophic microbes. Laminarin depolymerization catalyzed by microbial extracellular enzymes initiates remineralization, a key process in ocean biogeochemical cycles. Here, we described a glycoside hydrolase 16 (GH16) family laminarinase from a marine algae-associated flavobacterium at the biochemical and structural levels. We found that the endolytic enzyme cleaved laminarin with a preference for beta-1,3-glycoside linkages and showed transglycosylation activity across a broad range of acceptors. We also solved and compared high-resolution crystal structures of laminarinase in the apo form and in complex with beta-1,3-tetrasaccharides, revealing an expanded catalytic cleft formed following substrate binding. Moreover, structure and mutagenesis studies identified multiple specific contacts between the enzyme and glucosyl residues essential for the substrate specificity for beta-1,3-glucan. These results provide novel insights into the structural requirements for substrate binding and catalysis of GH16 family laminarinase, enriching our understanding of bacterial utilization of algal laminarin.IMPORTANCE Heterotrophic bacterial communities are key players in marine biogeochemical cycling due to their ability to remineralize organic carbon. Processing of complex organic matter requires heterotrophic bacteria to produce extracellular enzymes with precise specificity to depolymerize substrates to sizes sufficiently small for uptake. Thus, extracellular enzymatic hydrolysis initiates microbe-driven heterotrophic carbon cycling. In this study, based on biochemical and structural analyses, we revealed the depolymerization mechanism of beta-1, 3-glucan, a carbon reserve in algae, by laminarinase from an alga-associated marine flavobacterium. The findings provide new insights into the substrate recognition and catalysis of bacterial laminarinase and promote a better understanding of how extracellular enzymes are involved in organic matter cycling.
		+
		+	Molecular basis for substrate recognition and catalysis by a marine bacterial laminarinase.,Yang J, Xu Y, Miyakawa T, Long L, Tanokura M Appl Environ Microbiol. 2020 Sep 11. pii: AEM.01796-20. doi:, 10.1128/AEM.01796-20. PMID:32917756<ref>PMID:32917756</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jhj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:18, 30 September 2020

OCA — Wed, 30 Sep 2020 07:18:50 GMT

←Older revision		Revision as of 07:18, 30 September 2020
Line 3:		Line 3:
	<StructureSection load='6jhj' size='340' side='right'caption='[[6jhj]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='6jhj' size='340' side='right'caption='[[6jhj]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jhj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JHJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jhj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquimarina Aquimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JHJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhj OCA], [http://pdbe.org/6jhj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhj RCSB], [http://www.ebi.ac.uk/pdbsum/6jhj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhj 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=6jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhj OCA], [http://pdbe.org/6jhj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhj RCSB], [http://www.ebi.ac.uk/pdbsum/6jhj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhj ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquimarina]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Jian~~, Y]]	+	[[Category: Long, L]]
-	[[Category: ~~Lijuan~~, L]]	+	[[Category: Miyakawa, T]]
-	[[Category: ~~Masaru~~, T]]	+	[[Category: Tanokura, M]]
-	[[Category: ~~Takuya~~, M]]	+	[[Category: Xu, Y]]
-	[[Category: ~~Yuqun~~, X]]	+	[[Category: Yang, J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 07:05, 3 April 2019

OCA — Wed, 03 Apr 2019 07:05:02 GMT

←Older revision		Revision as of 07:05, 3 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jhj is ~~ON HOLD~~	+	==Structure of Marine bacterial laminarinase mutant-E135A==
-		+	<StructureSection load='6jhj' size='340' side='right'caption='[[6jhj]], [[Resolution\|resolution]] 1.69Å' scene=''>
-	~~Authors~~: ~~Jian~~, Y., ~~Yuqun, X~~., ~~Takuya, M~~., ~~Masaru, T~~., ~~Lijuan, L~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jhj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JHJ FirstGlance]. <br>
-	~~Description: Structure of Marine bacterial laminarinase mutant-E135A~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhj OCA], [http://pdbe.org/6jhj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhj RCSB], [http://www.ebi.ac.uk/pdbsum/6jhj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhj ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Jian, Y]]		[[Category: Jian, Y]]
	[[Category: Lijuan, L]]		[[Category: Lijuan, L]]
		+	[[Category: Masaru, T]]
	[[Category: Takuya, M]]		[[Category: Takuya, M]]
	[[Category: Yuqun, X]]		[[Category: Yuqun, X]]
-	[[Category: ~~Masaru, T~~]]	+	[[Category: Hydrolase]]

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

OCA — Wed, 27 Feb 2019 13:36:38 GMT

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

←Older revision

Revision as of 13:36, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6jhj is ON HOLD Authors: Jian, Y., Yuqun, X., Takuya, M., Masaru, T., Lijuan, L. Description: Structure of Marine bacterial laminarinase mutant-E13...

OCA — Wed, 27 Feb 2019 13:36:36 GMT

New page: '''Unreleased structure''' The entry 6jhj is ON HOLD Authors: Jian, Y., Yuqun, X., Takuya, M., Masaru, T., Lijuan, L. Description: Structure of Marine bacterial laminarinase mutant-E13...

New page

'''Unreleased structure'''

The entry 6jhj is ON HOLD

Authors: Jian, Y., Yuqun, X., Takuya, M., Masaru, T., Lijuan, L.

Description: Structure of Marine bacterial laminarinase mutant-E135A
[[Category: Unreleased Structures]]
[[Category: Jian, Y]]
[[Category: Lijuan, L]]
[[Category: Takuya, M]]
[[Category: Yuqun, X]]
[[Category: Masaru, T]]