5k3e: Difference between revisions
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==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - Cocrystallized== | ==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - Cocrystallized== | ||
<StructureSection load='5k3e' size='340' side='right' caption='[[5k3e]], [[Resolution|resolution]] 1.54Å' scene=''> | <StructureSection load='5k3e' size='340' side='right'caption='[[5k3e]], [[Resolution|resolution]] 1.54Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5k3e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3E OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[5k3e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhopa Rhopa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K3E FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene></td></tr> | </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=GOA:GLYCOLIC+ACID'>GOA</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k3a|5k3a]], [[5k3b|5k3b]], [[5k3c|5k3c]], [[5k3d|5k3d]], [[5k3f|5k3f]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k3a|5k3a]], [[5k3b|5k3b]], [[5k3c|5k3c]], [[5k3d|5k3d]], [[5k3f|5k3f]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPA1163 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=258594 RHOPA])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Haloacetate_dehalogenase Haloacetate dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.3 3.8.1.3] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Haloacetate_dehalogenase Haloacetate dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.3 3.8.1.3] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3e OCA], [http://pdbe.org/5k3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3e RCSB], [http://www.ebi.ac.uk/pdbsum/5k3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3e ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5k3e" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5k3e" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Haloacetate dehalogenase]] | [[Category: Haloacetate dehalogenase]] | ||
[[Category: Large Structures]] | |||
[[Category: Rhopa]] | |||
[[Category: Kim, T H]] | [[Category: Kim, T H]] | ||
[[Category: Mehrabi, P]] | [[Category: Mehrabi, P]] | ||
Revision as of 12:17, 25 June 2020
Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - CocrystallizedCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate - Cocrystallized
Structural highlights
Function[DEHA_RHOPA] Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has lower activity towards bromoacetate and chloroacetate.[1] [2] Publication Abstract from PubMedFreeze-trapping x-ray crystallography, nuclear magnetic resonance, and computational techniques reveal the distribution of states and their interconversion rates along the reaction pathway of a bacterial homodimeric enzyme, fluoroacetate dehalogenase (FAcD). The crystal structure of apo-FAcD exhibits asymmetry around the dimer interface and cap domain, priming one protomer for substrate binding. This asymmetry is dynamically averaged through conformational exchange on a millisecond time scale. During catalysis, the protomer conformational exchange rate becomes enhanced, the empty protomer exhibits increased local disorder, and water egresses. Computational studies identify allosteric pathways between protomers. Water release and enhanced dynamics associated with catalysis compensate for entropic losses from substrate binding while facilitating sampling of the transition state. The studies provide insights into how substrate-coupled allosteric modulation of structure and dynamics facilitates catalysis in a homodimeric enzyme. The role of dimer asymmetry and protomer dynamics in enzyme catalysis.,Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomes R, Prosser RS, Pai EF Science. 2017 Jan 20;355(6322). pii: eaag2355. doi: 10.1126/science.aag2355. PMID:28104837[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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