7xtf - Revision history

OCA at 11:45, 23 October 2024

2024-10-23T11:45:37Z

← Older revision		Revision as of 11:45, 23 October 2024
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	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.		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>		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>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 18:00, 29 November 2023

2023-11-29T18:00:12Z

← Older revision		Revision as of 18:00, 29 November 2023
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	==Crystal Structure of PL-5 family polysaccharide lyase PanPL-Y226F mutant from Pandoraea apista in apo form at pH5.5==		==Crystal Structure of PL-5 family polysaccharide lyase PanPL-Y226F mutant from Pandoraea apista in apo form at pH5.5==
	<StructureSection load='7xtf' size='340' side='right'caption='[[7xtf]]' scene=''>		<StructureSection load='7xtf' size='340' side='right'caption='[[7xtf]], [[Resolution\|resolution]] 1.73Å' 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=7XTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XTF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7xtf]] 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=7XTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XTF 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=7xtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xtf OCA], [https://pdbe.org/7xtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xtf RCSB], [https://www.ebi.ac.uk/pdbsum/7xtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xtf 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]] 1.73Å</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=EDO:1,2-ETHANEDIOL'>EDO</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=7xtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xtf OCA], [https://pdbe.org/7xtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xtf RCSB], [https://www.ebi.ac.uk/pdbsum/7xtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xtf 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 7xtf" 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

2022-08-10T05:02:31Z

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

	~~The entry~~ 7xtf is ~~ON HOLD until Paper Publication~~		==Crystal Structure of PL-5 family polysaccharide lyase PanPL-Y226F mutant from Pandoraea apista in apo form at pH5.5==
			<StructureSection load='7xtf' size='340' side='right'caption='[[7xtf]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XTF 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=7xtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xtf OCA], [https://pdbe.org/7xtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xtf RCSB], [https://www.ebi.ac.uk/pdbsum/7xtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xtf ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Acharya R]]
			[[Category: Dash P]]

OCA at 06:06, 29 June 2022

2022-06-29T06:06:43Z

← Older revision		Revision as of 06:06, 29 June 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2022-05-25T06:47:13Z

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

← Older revision	Revision as of 06:47, 25 May 2022
(No difference)

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

2022-05-25T06:47:12Z

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

New page

'''Unreleased structure'''

The entry 7xtf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]