3r3x: Difference between revisions

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 <StructureSection load='3r3x' size='340' side='right'caption='[[3r3x]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3r3x]] is a 2 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=3R3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R3X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3r3x]] 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=3R3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R3X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BXA:BROMOACETIC+ACID'>BXA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r3u|3r3u]], [[3r3v|3r3v]], [[3r3w|3r3w]], [[3r3y|3r3y]], [[3r3z|3r3z]], [[3r40|3r40]], [[3r41|3r41]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BXA:BROMOACETIC+ACID'>BXA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-<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'>[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'>[https://proteopedia.org/fgij/fg.htm?mol=3r3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r3x OCA], [https://pdbe.org/3r3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r3x RCSB], [https://www.ebi.ac.uk/pdbsum/3r3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r3x 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>
+[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 ==
-The 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<ref>PMID:21510690</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3r3x" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 28: / Line 17: @@
 __TOC__
 </StructureSection>
-[[Category: Rhodobacillus palustris molisch 1907]]
-[[Category: Haloacetate dehalogenase]]
 [[Category: Large Structures]]
-[[Category: Chan, P W.Y]]
+[[Category: Rhodopseudomonas palustris]]
-[[Category: Edwards, E A]]
+[[Category: Chan PWY]]
-[[Category: Pai, E F]]
+[[Category: Edwards EA]]
-[[Category: Yakunin, A F]]
+[[Category: Pai EF]]
-[[Category: Alpha/beta hydrolase]]
+[[Category: Yakunin AF]]
-[[Category: Defluorinase]]
-[[Category: Facd]]
-[[Category: Hydrolase]]