7wxl: Difference between revisions
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==Crystal Structure of PL-5 family polysaccharide lyase PanPL from Pandoraea apista at pH5.5 in apo form== | ==Crystal Structure of PL-5 family polysaccharide lyase PanPL from Pandoraea apista at pH5.5 in apo form== | ||
<StructureSection load='7wxl' size='340' side='right'caption='[[7wxl]]' scene=''> | <StructureSection load='7wxl' size='340' side='right'caption='[[7wxl]], [[Resolution|resolution]] 1.45Å' 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=7WXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WXL FirstGlance]. <br> | <table><tr><td colspan='2'>[[7wxl]] 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=7WXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WXL 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=7wxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wxl OCA], [https://pdbe.org/7wxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wxl RCSB], [https://www.ebi.ac.uk/pdbsum/7wxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wxl 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]] 1.45Å</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=7wxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wxl OCA], [https://pdbe.org/7wxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wxl RCSB], [https://www.ebi.ac.uk/pdbsum/7wxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wxl 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 7wxl" 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]] | ||
Revision as of 17:45, 29 November 2023
Crystal Structure of PL-5 family polysaccharide lyase PanPL from Pandoraea apista at pH5.5 in apo form
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