3r3u: Difference between revisions
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==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/apo== | ==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/apo== | ||
<StructureSection load='3r3u' size='340' side='right' caption='[[3r3u]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='3r3u' size='340' side='right'caption='[[3r3u]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3r3u]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3r3u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhodobacillus_palustris"_molisch_1907 "rhodobacillus palustris" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R3U 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=NI:NICKEL+(II)+ION'>NI</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=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3r41|3r41]], [[3r3v|3r3v]], [[3r3w|3r3w]], [[3r3x|3r3x]], [[3r3y|3r3y]], [[3r3z|3r3z]], [[3r40|3r40]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r41|3r41]], [[3r3v|3r3v]], [[3r3w|3r3w]], [[3r3x|3r3x]], [[3r3y|3r3y]], [[3r3z|3r3z]], [[3r40|3r40]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPA1163 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPA1163 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1076 "Rhodobacillus palustris" Molisch 1907])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Haloacetate_dehalogenase Haloacetate dehalogenase], with EC number [https://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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3r3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r3u OCA], [https://pdbe.org/3r3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r3u RCSB], [https://www.ebi.ac.uk/pdbsum/3r3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r3u ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == 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;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Dehalogenase|Dehalogenase]] | *[[Dehalogenase 3D structures|Dehalogenase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Rhodobacillus palustris molisch 1907]] | [[Category: Rhodobacillus palustris molisch 1907]] | ||
[[Category: Haloacetate dehalogenase]] | [[Category: Haloacetate dehalogenase]] | ||
[[Category: Large Structures]] | |||
[[Category: Chan, P W.Y]] | [[Category: Chan, P W.Y]] | ||
[[Category: Edwards, E A]] | [[Category: Edwards, E A]] | ||
Revision as of 08:47, 15 June 2022
Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/apoCrystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/apo
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 PubMedThe carbon-fluorine bond is the strongest covalent bond in organic chemistry, yet fluoroacetate dehalogenases can readily hydrolyze this bond under mild physiological conditions. Elucidating the molecular basis of this rare biocatalytic activity will provide the fundamental chemical insights into how this formidable feat is achieved. Here, we present a series of high-resolution (1.15-1.80 A) crystal structures of a fluoroacetate dehalogenase, capturing snapshots along the defluorination reaction: the free enzyme, enzyme-fluoroacetate Michaelis complex, glycolyl-enzyme covalent intermediate, and enzyme-product complex. We demonstrate that enzymatic defluorination requires a halide pocket that not only supplies three hydrogen bonds to stabilize the fluoride ion but also is finely tailored for the smaller fluorine halogen atom to establish selectivity toward fluorinated substrates. We have further uncovered dynamics near the active site which may play pivotal roles in enzymatic defluorination. These findings may ultimately lead to the development of novel defluorinases that will enable the biotransformation of more complex fluorinated organic compounds, which in turn will assist the synthesis, detoxification, biodegradation, disposal, recycling, and regulatory strategies for the growing markets of organofluorines across major industrial sectors. Mapping the Reaction Coordinates of Enzymatic Defluorination.,Chan PW, Yakunin AF, Edwards EA, Pai EF J Am Chem Soc. 2011 Apr 21. PMID:21510690[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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