OCA at 16:24, 29 November 2023

2023-11-29T16:24:09Z

← Older revision		Revision as of 16:24, 29 November 2023
Line 1:		Line 1:

	==CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid==		==CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid==
	<StructureSection load='7d2a' size='340' side='right'caption='[[7d2a]]' scene=''>		<StructureSection load='7d2a' size='340' side='right'caption='[[7d2a]], [[Resolution\|resolution]] 1.57Å' 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=7D2A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7D2A FirstGlance]. <br>		<table><tr><td colspan='2'>[[7d2a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Persicobacter_sp._CCB-QB2 Persicobacter sp. CCB-QB2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D2A 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=7d2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d2a OCA], [~~http~~://pdbe.org/7d2a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7d2a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7d2a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7d2a ProSAT]</span></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]] 1.57Å</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>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAW:4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC+ACID'>MAW</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=7d2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d2a OCA], [https://pdbe.org/7d2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d2a RCSB], [https://www.ebi.ac.uk/pdbsum/7d2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d2a ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A0A3B6UEP6_9BACT A0A3B6UEP6_9BACT]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The alginate lyase AlyQ from Persicobacter sp. CCB-QB2 is a three-domained enzyme with a carbohydrate-binding module (CBM) from family 32. The CBM32 domain, AlyQB, binds enzymatically cleaved but not intact alginate. Co-crystallisation of AlyQB with the cleaved alginate reveals that it binds to the 4,5-unsaturated mannuronic acid of the non-reducing end. The binding pocket contains a conserved R248 that interacts with the sugar's carboxyl group, as well as an invariant W303 that stacks against the unsaturated pyranose ring. Targeting specifically the non-reducing end is more efficient than the reducing end since the latter consists of a mixture of mannuronic acid and guluronic acid. AlyQB also seems unable to bind these two saturated sugars as they contain OH groups that will clash with the pocket. Docking analysis of YeCBM32, which binds oligogalacturonic acid, shows that the stacking of the pyranose ring is shifted in order to accommodate the sugar's axial C1-OH, and its R69 is accordingly elevated to bind the sugar's carboxyl group. Unlike AlyQB, YeCBM32's binding pocket is able to accommodate both saturated and unsaturated galacturonic acid.

			Structural basis for binding uronic acids by family 32 carbohydrate-binding modules.,Teh AH, Sim PF, Hisano T Biochem Biophys Res Commun. 2020 Dec 10;533(3):257-261. doi:, 10.1016/j.bbrc.2020.09.064. Epub 2020 Oct 1. PMID:33010888<ref>PMID:33010888</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7d2a" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
			[[Category: Persicobacter sp. CCB-QB2]]
	[[Category: Sim PF]]		[[Category: Sim PF]]
	[[Category: Teh AH]]		[[Category: Teh AH]]

OCA at 06:48, 30 December 2020

2020-12-30T06:48:52Z

← Older revision		Revision as of 06:48, 30 December 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7d2a is ~~ON HOLD~~		==CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid==
			<StructureSection load='7d2a' size='340' side='right'caption='[[7d2a]]' scene=''>
	~~Authors~~: ~~Teh~~, A.H., ~~Sim~~, P.F.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D2A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D2A FirstGlance]. <br>
	~~Description~~: ~~CBM32 of AlyQ in complex with 4~~,5-~~unsaturated mannuronic acid~~		</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=7d2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d2a OCA], [http://pdbe.org/7d2a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d2a RCSB], [http://www.ebi.ac.uk/pdbsum/7d2a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d2a ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Teh, A.H~~]]		__TOC__
	[[Category: ~~Sim, P.F~~]]		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Sim PF]]
			[[Category: Teh AH]]

OCA: Protected "7d2a" [edit=sysop:move=sysop]

2020-09-23T08:58:18Z

Protected "7d2a" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:58, 23 September 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7d2a is ON HOLD Authors: Teh, A.H., Sim, P.F. Description: CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid [[Category: Unreleased Str...

2020-09-23T08:58:17Z

New page: '''Unreleased structure''' The entry 7d2a is ON HOLD Authors: Teh, A.H., Sim, P.F. Description: CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid [[Category: Unreleased Str...

New page

'''Unreleased structure'''

The entry 7d2a is ON HOLD

Authors: Teh, A.H., Sim, P.F.

Description: CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid
[[Category: Unreleased Structures]]
[[Category: Teh, A.H]]
[[Category: Sim, P.F]]

7d2a - Revision history

OCA at 16:24, 29 November 2023

OCA at 06:48, 30 December 2020

OCA: Protected "7d2a" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7d2a is ON HOLD Authors: Teh, A.H., Sim, P.F. Description: CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid [[Category: Unreleased Str...