OCA at 17:45, 29 November 2023

OCA — Wed, 29 Nov 2023 17:45:39 GMT

←Older revision		Revision as of 17:45, 29 November 2023
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	==Crystal Structure of PL-5 family polysaccharide lyase PanPL-H172A mutant from Pandoraea apista in apo form==		==Crystal Structure of PL-5 family polysaccharide lyase PanPL-H172A mutant from Pandoraea apista in apo form==
-	<StructureSection load='7wxq' size='340' side='right'caption='[[7wxq]]' scene=''>	+	<StructureSection load='7wxq' size='340' side='right'caption='[[7wxq]], [[Resolution\|resolution]] 2.03Å' 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=7WXQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WXQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7wxq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pandoraea_apista Pandoraea apista]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WXQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WXQ 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=7wxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wxq OCA], [https://pdbe.org/7wxq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wxq RCSB], [https://www.ebi.ac.uk/pdbsum/7wxq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wxq 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]] 2.03Å</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></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=7wxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wxq OCA], [https://pdbe.org/7wxq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wxq RCSB], [https://www.ebi.ac.uk/pdbsum/7wxq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wxq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A5E5PAL9_9BURK A0A5E5PAL9_9BURK]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dynamics is an essential process to drive an enzyme to perform a function. When a protein sequence encodes for its three-dimensional structure and hence its function, it essentially defines the intrinsic dynamics of the molecule. The static X-ray crystal structure was thought to shed little insight into the molecule's dynamics until the recently available tool "Ensemble refinement" (ER). Here, we report the structure-function-dynamics of PanPL, an alginate-specific, endolytic, allosteric polysaccharide lyase belonging to the PL-5 family from Pandoraea apista. The crystal structures determined in apo and tetra-ManA bound forms reveal that the PanPL maintains a closed state with an N-terminal loop lid (N-loop-lid) arched over the active site. The B-factor analyses and ER congruently reveal how pH influences the functionally relevant atomic fluctuations at the N-loop-lid. The ER unveils enhanced fluctuations at the N-loop-lid upon substrate binding. The normal-mode analysis finds that the functional states are confined. The 1 mus simulation study suggests the existence of a hidden open state. The longer N-loop-lid selects a mechanism to adopt a closed state and undergo fluctuations to facilitate the substrate binding. Here, our work demonstrates the distinct modes of dynamics; both intrinsic and substrate-induced conformational changes are vital for enzyme functioning and allostery.
		+
		+	Distinct Modes of Hidden Structural Dynamics in the Functioning of an Allosteric Polysaccharide Lyase.,Dash P, Acharya R ACS Cent Sci. 2022 Jul 27;8(7):933-947. doi: 10.1021/acscentsci.2c00277. Epub, 2022 Jul 6. PMID:35912344<ref>PMID:35912344</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7wxq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pandoraea apista]]
	[[Category: Acharya R]]		[[Category: Acharya R]]
	[[Category: Dash P]]		[[Category: Dash P]]

OCA at 05:02, 10 August 2022

OCA — Wed, 10 Aug 2022 05:02:19 GMT

←Older revision		Revision as of 05:02, 10 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7wxq ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of PL-5 family polysaccharide lyase PanPL-H172A mutant from Pandoraea apista in apo form==
-		+	<StructureSection load='7wxq' size='340' side='right'caption='[[7wxq]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WXQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WXQ FirstGlance]. <br>
-	~~Description~~:	+	</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=7wxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wxq OCA], [https://pdbe.org/7wxq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wxq RCSB], [https://www.ebi.ac.uk/pdbsum/7wxq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wxq ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Acharya R]]
		+	[[Category: Dash P]]

OCA at 09:39, 30 March 2022

OCA — Wed, 30 Mar 2022 09:39:40 GMT

←Older revision		Revision as of 09:39, 30 March 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wxq is ON HOLD	+	The entry 7wxq is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 23 Feb 2022 06:41:43 GMT

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

←Older revision

Revision as of 06:41, 23 February 2022

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

OCA — Wed, 23 Feb 2022 06:41:42 GMT

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

New page

'''Unreleased structure'''

The entry 7wxq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7wxq - Revision history

OCA at 17:45, 29 November 2023

OCA at 05:02, 10 August 2022

OCA at 09:39, 30 March 2022

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

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