7c8f - Revision history

OCA at 15:59, 29 November 2023

2023-11-29T15:59:03Z

← Older revision		Revision as of 15:59, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7c8f' size='340' side='right'caption='[[7c8f]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='7c8f' size='340' side='right'caption='[[7c8f]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7c8f]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Psychromonas_sp. Psychromonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7C8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[7c8f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Psychromonas_sp. Psychromonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C8F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=~~MLI~~:~~MALONATE~~+~~ION~~'>~~MLI~~</scene>, <scene name='pdbligand=~~BEM~~:~~BETA-D-MANNURONIC~~+~~ACID~~'>~~BEM~~</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]] 1.461Å</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=7c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8f OCA], [~~http~~://pdbe.org/7c8f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7c8f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7c8f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8f ProSAT]</span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=7c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8f OCA], [https://pdbe.org/7c8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c8f RCSB], [https://www.ebi.ac.uk/pdbsum/7c8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8f ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 23:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Psychromonas sp]]		[[Category: Psychromonas sp]]
	[[Category: Chen~~, X L~~]]		[[Category: Chen XL]]
	[[Category: Wang, P]]		[[Category: Wang P]]
	[[Category: Xu, F]]		[[Category: Xu F]]
	[[Category: Zhang~~, Y Z]]~~		[[Category: Zhang YZ]]
	~~[[Category: Alginate]]~~
	~~[[Category: Alginate lyase]]~~
	~~[[Category: Lyase~~]]

OCA at 06:23, 14 October 2020

2020-10-14T06:23:00Z

← Older revision		Revision as of 06:23, 14 October 2020
Line 1:		Line 1:

	==Structure of alginate lyase AlyC3 in complex with dimannuronate(2M)==		==Structure of alginate lyase AlyC3 in complex with dimannuronate(2M)==
	<StructureSection load='7c8f' size='340' side='right'caption='[[7c8f]]' scene=''>		<StructureSection load='7c8f' size='340' side='right'caption='[[7c8f]], [[Resolution\|resolution]] 1.46Å' 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=7C8F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7C8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[7c8f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Psychromonas_sp. Psychromonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7C8F 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=7c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8f OCA], [http://pdbe.org/7c8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c8f RCSB], [http://www.ebi.ac.uk/pdbsum/7c8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8f 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=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</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=7c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8f OCA], [http://pdbe.org/7c8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c8f RCSB], [http://www.ebi.ac.uk/pdbsum/7c8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8f ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Alginate lyases play important roles in alginate degradation in the ocean. Although a large number of alginate lyases have been characterized, little is yet known about those in extremely cold polar environments, which may have unique mechanisms for environmental adaptation and for alginate degradation. Here, we report the characterization of a novel PL7 alginate lyase AlyC3 from Psychromonas sp. C-3 isolated from the Arctic brown alga Laminaria, including its phylogenetic classification, catalytic properties and structure. We propose the establishment of a new PM-specific subfamily of PL7 (subfamily 6) represented by AlyC3 based on phylogenetic analysis and enzymatic properties. Structural and biochemical analyses showed that AlyC3 is a dimer, representing the first dimeric endo-alginate lyase structure. AlyC3 is activated by NaCl and adopts a novel salt-activated mechanism, that is, salinity adjusts the enzymatic activity by affecting its aggregation states. We further solved the structure of an inactive mutant H127A/Y244A in complex with a dimannuronate molecule, and proposed the catalytic process of AlyC3 based on structural and biochemical analyses. We show that Arg82 and Tyr190 at the two ends of the catalytic canyon help the positioning of the repeated units of the substrate, and that His127, Tyr244, Arg78, and Gln125 mediate the catalytic reaction. Our study uncovers, for the first time, the amino acid residues for alginate positioning in an alginate lyase, and demonstrate that such residues involved in alginate positioning are conserved in other alginate lyases. This study provides a better understanding of the mechanisms of alginate degradation by alginate lyases.

			Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic.,Xu F, Chen XL, Sun XH, Dong F, Li CY, Li PY, Ding H, Chen Y, Zhang YZ, Wang P J Biol Chem. 2020 Sep 23. pii: RA120.015106. doi: 10.1074/jbc.RA120.015106. PMID:32967968<ref>PMID:32967968</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7c8f" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen XL]]		[[Category: Psychromonas sp]]
	[[Category: Wang P]]		[[Category: Chen, X L]]
	[[Category: Xu F]]		[[Category: Wang, P]]
	[[Category: Zhang YZ]]		[[Category: Xu, F]]
			[[Category: Zhang, Y Z]]
			[[Category: Alginate]]
			[[Category: Alginate lyase]]
			[[Category: Lyase]]

OCA at 06:22, 7 October 2020

2020-10-07T06:22:27Z

← Older revision		Revision as of 06:22, 7 October 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7c8f is ~~ON HOLD until Paper Publication~~		==Structure of alginate lyase AlyC3 in complex with dimannuronate(2M)==
			<StructureSection load='7c8f' size='340' side='right'caption='[[7c8f]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7C8F 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=7c8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8f OCA], [http://pdbe.org/7c8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c8f RCSB], [http://www.ebi.ac.uk/pdbsum/7c8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8f ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Chen XL]]
			[[Category: Wang P]]
			[[Category: Xu F]]
			[[Category: Zhang YZ]]

OCA at 04:06, 5 August 2020

2020-08-05T04:06:02Z

← Older revision		Revision as of 04:06, 5 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7c8f is ON HOLD		The entry 7c8f is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7c8f" [edit=sysop:move=sysop]

2020-06-10T05:18:03Z

Protected "7c8f" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:18, 10 June 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7c8f is ON HOLD Authors: Description: Category: Unreleased Structures

2020-06-10T05:18:01Z

New page: '''Unreleased structure''' The entry 7c8f is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7c8f is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]