7l0m: Difference between revisions

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<StructureSection load='7l0m' size='340' side='right'caption='[[7l0m]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='7l0m' size='340' side='right'caption='[[7l0m]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7l0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L0M FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L0M FirstGlance]. <br>
</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&#8491;</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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VO4:VANADATE+ION'>VO4</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=7l0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l0m OCA], [https://pdbe.org/7l0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l0m RCSB], [https://www.ebi.ac.uk/pdbsum/7l0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l0m 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=7l0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l0m OCA], [https://pdbe.org/7l0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l0m RCSB], [https://www.ebi.ac.uk/pdbsum/7l0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l0m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O68720_YERPE O68720_YERPE]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic pK a of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the variants show no structural perturbations but suggest an increased preference for the WPD-loop-closed conformation. Computational analysis confirms a shift in loop conformational equilibrium in favor of the closed conformation, arising from a combination of increased stability of the closed state and destabilization of the loop-open state. Simulations identify the origins of this population shift, revealing differences in the flexibility of the WPD-loop and neighboring regions. Our results demonstrate that changes to the pH dependency of catalysis by PTPs can result from small changes in amino acid composition in their WPD-loops affecting only loop dynamics and conformational equilibrium. The perturbation of kinetic pK a values of catalytic residues by nonchemical processes affords a means for nature to alter an enzyme's pH dependency by a less disruptive path than altering electrostatic networks around catalytic residues themselves.
Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases.,Shen R, Crean RM, Johnson SJ, Kamerlin SCL, Hengge AC JACS Au. 2021 May 24;1(5):646-659. doi: 10.1021/jacsau.1c00054. Epub 2021 Apr 23. PMID:34308419<ref>PMID:34308419</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7l0m" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Tyrosine phosphatase 3D structures|Tyrosine phosphatase 3D structures]]
*[[Tyrosine phosphatase 3D structures|Tyrosine phosphatase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Yersinia pestis]]
[[Category: Hengge AC]]
[[Category: Hengge AC]]
[[Category: Johnson SJ]]
[[Category: Johnson SJ]]
[[Category: Shen RD]]
[[Category: Shen RD]]
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