6m6p - Revision history

OCA at 15:19, 29 November 2023

2023-11-29T15:19:08Z

←Older revision		Revision as of 15:19, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='6m6p' size='340' side='right'caption='[[6m6p]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='6m6p' size='340' side='right'caption='[[6m6p]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m6p]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aquimarina_sp. Aquimarina sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M6P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6M6P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m6p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquimarina_sp. Aquimarina sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M6P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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]] 2.27Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6jh5\|6jh5]], [[6jhj\|6jhj]], [[6jia\|6jia]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [~~http~~://pdbe.org/6m6p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p 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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [https://pdbe.org/6m6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [https://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A6F9D674_9FLAO A0A6F9D674_9FLAO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6m6p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6m6p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Laminarase 3D structures\|Laminarase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 28:
	[[Category: Aquimarina sp]]		[[Category: Aquimarina sp]]
	[[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 07:06, 25 November 2020

2020-11-25T07:06:08Z

←Older revision		Revision as of 07:06, 25 November 2020
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[6m6p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquimarina_sp. Aquimarina sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M6P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M6P FirstGlance]. <br>		<table><tr><td colspan='2'>[[6m6p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquimarina_sp. Aquimarina sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M6P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M6P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jh5\|6jh5]], [[6jhj\|6jhj]], [[6jia\|6jia]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6jh5\|6jh5]], [[6jhj\|6jhj]], [[6jia\|6jia]]</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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [http://pdbe.org/6m6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [http://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p 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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [http://pdbe.org/6m6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [http://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:29, 7 October 2020

2020-10-07T06:29:46Z

←Older revision		Revision as of 06:29, 7 October 2020
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [http://pdbe.org/6m6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [http://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p 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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [http://pdbe.org/6m6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [http://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p 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 6m6p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:22, 30 September 2020

2020-09-30T07:22:29Z

←Older revision		Revision as of 07:22, 30 September 2020
Line 1:		Line 1:

	==Structure of Marine bacterial laminarinase mutant E135A in complex with 1,3-beta-cellotriosyl-glucose==		==Structure of Marine bacterial laminarinase mutant E135A in complex with 1,3-beta-cellotriosyl-glucose==
-	<StructureSection load='6m6p' size='340' side='right'caption='[[6m6p]]' scene=''>	+	<StructureSection load='6m6p' size='340' side='right'caption='[[6m6p]], [[Resolution\|resolution]] 2.27Å' 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=6M6P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M6P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m6p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquimarina_sp. Aquimarina sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M6P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M6P 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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [http://pdbe.org/6m6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [http://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jh5\|6jh5]], [[6jhj\|6jhj]], [[6jia\|6jia]]</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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [http://pdbe.org/6m6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [http://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquimarina sp]]
	[[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 11:09, 23 September 2020

2020-09-23T11:09:06Z

←Older revision		Revision as of 11:09, 23 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6m6p is ~~ON HOLD until Paper Publication~~	+	==Structure of Marine bacterial laminarinase mutant E135A in complex with 1,3-beta-cellotriosyl-glucose==
-		+	<StructureSection load='6m6p' size='340' side='right'caption='[[6m6p]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M6P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M6P FirstGlance]. <br>
-	~~Description~~:	+	</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=6m6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m6p OCA], [http://pdbe.org/6m6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m6p RCSB], [http://www.ebi.ac.uk/pdbsum/6m6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m6p ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Long L]]
		+	[[Category: Miyakawa T]]
		+	[[Category: Tanokura M]]
		+	[[Category: Xu Y]]
		+	[[Category: Yang J]]

OCA at 04:21, 6 May 2020

2020-05-06T04:21:01Z

←Older revision		Revision as of 04:21, 6 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6m6p is ON HOLD	+	The entry 6m6p is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6m6p" [edit=sysop:move=sysop]

2020-03-27T08:17:11Z

Protected "6m6p" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:17, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 6m6p is ON HOLD Authors: Description: Category: Unreleased Structures

2020-03-27T08:17:10Z

New page: '''Unreleased structure''' The entry 6m6p is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6m6p is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]