7vqm - Revision history

OCA at 17:30, 29 November 2023

OCA — Wed, 29 Nov 2023 17:30:38 GMT

←Older revision		Revision as of 17:30, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7vqm]] is a 4 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=7VQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VQM FirstGlance]. <br>		<table><tr><td colspan='2'>[[7vqm]] is a 4 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=7VQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VQM 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=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</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]] 2.4Å</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=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</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=7vqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vqm OCA], [https://pdbe.org/7vqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vqm RCSB], [https://www.ebi.ac.uk/pdbsum/7vqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vqm 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=7vqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vqm OCA], [https://pdbe.org/7vqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vqm RCSB], [https://www.ebi.ac.uk/pdbsum/7vqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vqm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:32, 7 December 2022

OCA — Wed, 07 Dec 2022 08:32:42 GMT

←Older revision		Revision as of 08:32, 7 December 2022
Line 1:		Line 1:

	==GH2 beta-galacturonate AqGalA in complex with galacturonide==		==GH2 beta-galacturonate AqGalA in complex with galacturonide==
-	<StructureSection load='7vqm' size='340' side='right'caption='[[7vqm]]' scene=''>	+	<StructureSection load='7vqm' size='340' side='right'caption='[[7vqm]], [[Resolution\|resolution]] 2.40Å' 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=7VQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vqm]] is a 4 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=7VQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VQM FirstGlance]. <br>
-	</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=7vqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vqm OCA], [https://pdbe.org/7vqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vqm RCSB], [https://www.ebi.ac.uk/pdbsum/7vqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vqm 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</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=7vqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vqm OCA], [https://pdbe.org/7vqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vqm RCSB], [https://www.ebi.ac.uk/pdbsum/7vqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vqm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Uronic acids are commonly found in marine polysaccharides and increase structural complexity and intrinsic recalcitrance to enzymatic attack. Glycoside hydrolase family 2 (GH2) includes proteins that target sugar conjugates with hexuronates and are involved in the catabolism and cycling of marine polysaccharides. Here, we report a novel GH2, AqGalA from a marine alga-associated Bacteroidetes organism with broad substrate specificity. Biochemical analyses revealed that AqGalA exhibits hydrolyzing activities against beta-galacturonide, beta-glucuronide, and beta-galactopyranoside via retaining mechanisms. We solved the AqGalA crystal structure in complex with galacturonic acid (GalA) and determined (via mutagenesis) that charge characteristics at uronate-binding subsites controlled substrate selectivity for uronide hydrolysis. Additionally, conformational flexibility of the AqGalA active-site pocket was proposed as a key component for broad substrate enzyme selectivity. Our AqGalA structural and functional data augment the current understanding of substrate recognition of GH2 enzymes and provide key insights into the bacterial use of uronic acid-containing polysaccharides. IMPORTANCE The decomposition of algal glycans driven by marine bacterial communities represents one of the largest heterotrophic transformations of organic matter fueling marine food webs and global carbon cycling. However, our knowledge on carbohydrate cycling is limited due to structural complexity of marine polysaccharides and the complicated enzymatic machinery of marine microbes. To degrade algal glycan, marine bacteria such as members of the Bacteroidetes produce a complex repertoire of carbohydrate-active enzymes (CAZymes) matching the structural specificities of the different carbohydrates. In this study, we investigated an extracellular GH2 beta-glycosidase, AqGalA from a marine Bacteroidetes organism, to identify the key components responsible for glycuronide recognition and hydrolysis. The broad substrate specificity of AqGalA against glycosides with diverse stereochemical substitutions indicates its potential in processing complex marine polysaccharides. Our findings promote a better understanding of microbially driven mechanisms of marine carbohydrate cycling.
		+
		+	Structural and Biochemical Basis of a Marine Bacterial Glycoside Hydrolase Family 2 beta-Glycosidase with Broad Substrate Specificity.,Yang J, Li S, Liu Y, Li R, Long L Appl Environ Microbiol. 2022 Jan 25;88(2):e0222621. doi: 10.1128/AEM.02226-21. , Epub 2021 Nov 24. PMID:34818100<ref>PMID:34818100</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vqm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquimarina sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Yang J]]		[[Category: Yang J]]

OCA at 12:39, 24 November 2021

OCA — Wed, 24 Nov 2021 12:39:46 GMT

←Older revision		Revision as of 12:39, 24 November 2021
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-	'''Unreleased structure'''

-	~~The entry 7vqm is ON HOLD~~	+	==GH2 beta-galacturonate AqGalA in complex with galacturonide==
-		+	<StructureSection load='7vqm' size='340' side='right'caption='[[7vqm]]' scene=''>
-	~~Authors: Yang, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VQM FirstGlance]. <br>
-	~~Description:~~ GH2 beta-galacturonate AqGalA in complex with galacturonide	+	</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=7vqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vqm OCA], [https://pdbe.org/7vqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vqm RCSB], [https://www.ebi.ac.uk/pdbsum/7vqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vqm ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Yang, J]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Yang J]]

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

OCA — Wed, 27 Oct 2021 12:53:05 GMT

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

←Older revision

Revision as of 12:53, 27 October 2021

OCA: New page: '''Unreleased structure''' The entry 7vqm is ON HOLD Authors: Yang, J. Description: GH2 beta-galacturonate AqGalA in complex with galacturonide Category: Unreleased Structures [[Ca...

OCA — Wed, 27 Oct 2021 12:53:03 GMT

New page: '''Unreleased structure''' The entry 7vqm is ON HOLD Authors: Yang, J. Description: GH2 beta-galacturonate AqGalA in complex with galacturonide Category: Unreleased Structures [[Ca...

New page

'''Unreleased structure'''

The entry 7vqm is ON HOLD

Authors: Yang, J.

Description: GH2 beta-galacturonate AqGalA in complex with galacturonide
[[Category: Unreleased Structures]]
[[Category: Yang, J]]