6qkt: Difference between revisions
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==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Tyr219Phe - Fluoroacetate soaked 24hr - Glycolate bound== | |||
<StructureSection load='6qkt' size='340' side='right'caption='[[6qkt]], [[Resolution|resolution]] 1.51Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6qkt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKT 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]] 1.512Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</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=6qkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkt OCA], [https://pdbe.org/6qkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qkt RCSB], [https://www.ebi.ac.uk/pdbsum/6qkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkt ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DEHA_RHOPA DEHA_RHOPA] Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has lower activity towards bromoacetate and chloroacetate.<ref>PMID:21510690</ref> <ref>PMID:21510690</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an inter-protomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by NMR and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function. | |||
Substrate-based Allosteric Regulation of a Homodimeric Enzyme.,Mehrabi P, Di Pietrantonio C, Kim TH, Sljoka A, Taverner K, Ing C, Kruglyak N, Pomes R, Pai EF, Prosser RS J Am Chem Soc. 2019 Jun 12. doi: 10.1021/jacs.9b03703. PMID:31188575<ref>PMID:31188575</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6qkt" style="background-color:#fffaf0;"></div> | ||
[[Category: Mehrabi | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Dehalogenase 3D structures|Dehalogenase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Rhodopseudomonas palustris]] | |||
[[Category: Kim TH]] | |||
[[Category: Mehrabi P]] | |||
[[Category: Pai EF]] | |||
[[Category: Prosser RS]] | |||
Latest revision as of 13:40, 15 November 2023
Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Tyr219Phe - Fluoroacetate soaked 24hr - Glycolate boundCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Tyr219Phe - Fluoroacetate soaked 24hr - Glycolate bound
Structural highlights
FunctionDEHA_RHOPA Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has lower activity towards bromoacetate and chloroacetate.[1] [2] Publication Abstract from PubMedMany enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an inter-protomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by NMR and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function. Substrate-based Allosteric Regulation of a Homodimeric Enzyme.,Mehrabi P, Di Pietrantonio C, Kim TH, Sljoka A, Taverner K, Ing C, Kruglyak N, Pomes R, Pai EF, Prosser RS J Am Chem Soc. 2019 Jun 12. doi: 10.1021/jacs.9b03703. PMID:31188575[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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