3r40 - Revision history

OCA at 10:52, 21 February 2024

2024-02-21T10:52:04Z

←Older revision		Revision as of 10:52, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3r40' size='340' side='right'caption='[[3r40]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='3r40' size='340' side='right'caption='[[3r40]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r40]] 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=3R40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R40 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r40]] 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=3R40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R40 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.05Å</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]], [[3r3x\|3r3x]], [[3r3y\|3r3y]], [[3r3z\|3r3z]], [[3r41\|3r41]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=3r40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r40 OCA], [https://pdbe.org/3r40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r40 RCSB], [https://www.ebi.ac.uk/pdbsum/3r40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r40 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=3r40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r40 OCA], [https://pdbe.org/3r40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r40 RCSB], [https://www.ebi.ac.uk/pdbsum/3r40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r40 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>	+	[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®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3r40" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Rhodobacillus palustris molisch 1907]]
-	[[Category: Haloacetate dehalogenase]]
	[[Category: Large Structures]]		[[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~~]]	+

OCA at 05:48, 15 June 2022

2022-06-15T05:48:02Z

←Older revision		Revision as of 05:48, 15 June 2022
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	==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo==		==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo==
-	<StructureSection load='3r40' size='340' side='right' caption='[[3r40]], [[Resolution\|resolution]] 1.05Å' scene=''>	+	<StructureSection load='3r40' size='340' side='right'caption='[[3r40]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r40]] is a 2 chain structure with sequence from [~~http~~://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=3R40 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3R40 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r40]] 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=3R40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R40 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r3u\|3r3u]], [[3r3v\|3r3v]], [[3r3w\|3r3w]], [[3r3x\|3r3x]], [[3r3y\|3r3y]], [[3r3z\|3r3z]], [[3r41\|3r41]]</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]], [[3r3x\|3r3x]], [[3r3y\|3r3y]], [[3r3z\|3r3z]], [[3r41\|3r41]]</div></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=1076 "Rhodobacillus palustris" Molisch 1907])</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'>[~~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'>[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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3r40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r40 OCA], [~~http~~://pdbe.org/3r40 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3r40 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3r40 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3r40 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=3r40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r40 OCA], [https://pdbe.org/3r40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r40 RCSB], [https://www.ebi.ac.uk/pdbsum/3r40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r40 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Dehalogenase\|Dehalogenase]]	+	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 30:
	[[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]]

OCA at 15:43, 4 August 2016

2016-08-04T15:43:48Z

←Older revision		Revision as of 15:43, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo==		==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo==
	<StructureSection load='3r40' size='340' side='right' caption='[[3r40]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='3r40' size='340' side='right' caption='[[3r40]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r40]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodopseudomonas_palustris Rhodopseudomonas~~ palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R40 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r40]] is a 2 chain structure with sequence from [http://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=3R40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R40 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r3u\|3r3u]], [[3r3v\|3r3v]], [[3r3w\|3r3w]], [[3r3x\|3r3x]], [[3r3y\|3r3y]], [[3r3z\|3r3z]], [[3r41\|3r41]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r3u\|3r3u]], [[3r3v\|3r3v]], [[3r3w\|3r3w]], [[3r3x\|3r3x]], [[3r3y\|3r3y]], [[3r3z\|3r3z]], [[3r41\|3r41]]</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=1076 ~~Rhodopseudomonas~~ palustris])</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=1076 "Rhodobacillus palustris" Molisch 1907])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3r40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r40 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r40 RCSB], [http://www.ebi.ac.uk/pdbsum/3r40 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3r40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r40 OCA], [http://pdbe.org/3r40 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r40 RCSB], [http://www.ebi.ac.uk/pdbsum/3r40 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3r40 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3r40" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Rhodobacillus palustris molisch 1907]]
	[[Category: Haloacetate dehalogenase]]		[[Category: Haloacetate dehalogenase]]
-	[[Category: Rhodopseudomonas palustris]]
	[[Category: Chan, P W.Y]]		[[Category: Chan, P W.Y]]
	[[Category: Edwards, E A]]		[[Category: Edwards, E A]]

OCA at 16:35, 24 December 2014

2014-12-24T16:35:45Z

←Older revision		Revision as of 16:35, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3r40\| PDB=3r40 \| SCENE= }}~~	+	==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo==
-	===Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo===	+	<StructureSection load='3r40' size='340' side='right' caption='[[3r40]], [[Resolution\|resolution]] 1.05Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21510690}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3r40]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R40 FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r3u\|3r3u]], [[3r3v\|3r3v]], [[3r3w\|3r3w]], [[3r3x\|3r3x]], [[3r3y\|3r3y]], [[3r3z\|3r3z]], [[3r41\|3r41]]</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=1076 Rhodopseudomonas palustris])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3r40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r40 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r40 RCSB], [http://www.ebi.ac.uk/pdbsum/3r40 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://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>		[[http://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>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3r40]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3R40 OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:021510690</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Dehalogenase\|Dehalogenase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Haloacetate dehalogenase]]		[[Category: Haloacetate dehalogenase]]
	[[Category: Rhodopseudomonas palustris]]		[[Category: Rhodopseudomonas palustris]]
-	[[Category: Chan, P W.Y.]]	+	[[Category: Chan, P W.Y]]
-	[[Category: Edwards, E A.]]	+	[[Category: Edwards, E A]]
-	[[Category: Pai, E F.]]	+	[[Category: Pai, E F]]
-	[[Category: Yakunin, A F.]]	+	[[Category: Yakunin, A F]]
	[[Category: Alpha/beta hydrolase]]		[[Category: Alpha/beta hydrolase]]
	[[Category: Defluorinase]]		[[Category: Defluorinase]]
	[[Category: Facd]]		[[Category: Facd]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 07:48, 16 May 2013

2013-05-16T07:48:20Z

←Older revision		Revision as of 07:48, 16 May 2013
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-	[[Image:3r40.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3r40", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3r40\| PDB=3r40 \| SCENE= }}		{{STRUCTURE_3r40\| PDB=3r40 \| SCENE= }}
-
	===Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo===		===Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo===
		+	{{ABSTRACT_PUBMED_21510690}}

-		+	==Function==
-	~~<!--~~	+	[[http://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>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21510690}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 21510690 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21510690}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021510690</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021510690</ref><references group="xtra"/><references/>
	[[Category: Haloacetate dehalogenase]]		[[Category: Haloacetate dehalogenase]]
	[[Category: Rhodopseudomonas palustris]]		[[Category: Rhodopseudomonas palustris]]
Line 29:		Line 17:
	[[Category: Pai, E F.]]		[[Category: Pai, E F.]]
	[[Category: Yakunin, A F.]]		[[Category: Yakunin, A F.]]
		+	[[Category: Alpha/beta hydrolase]]
		+	[[Category: Defluorinase]]
		+	[[Category: Facd]]
		+	[[Category: Hydrolase]]

OCA at 04:49, 1 June 2011

2011-06-01T04:49:30Z

←Older revision		Revision as of 04:49, 1 June 2011
Line 1:		Line 1:
-	[[Image:3r40.~~jpg~~\|left\|200px]]	+	[[Image:3r40.png\|left\|200px]]

	<!--		<!--

OCA at 06:53, 4 May 2011

2011-05-04T06:53:00Z

←Older revision		Revision as of 06:53, 4 May 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3r40.jpg\|left\|200px]]

-	The ~~entry 3r40~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3r40", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3r40\| PDB=3r40 \| SCENE= }}

-	~~Authors: Chan, P.W.Y., Yakunin, A.F., Edwards, E.A., Pai, E.F.~~	+	===Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/apo===

-	~~Description~~: ~~Crystal Structure of~~ the ~~Fluoroacetate Dehalogenase RPA1163~~ -~~Asp110Asn~~/~~apo~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21510690}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21510690 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21510690}}
		+
		+	==About this Structure==
		+	[[3r40]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R40 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021510690</ref><references group="xtra"/>
		+	[[Category: Haloacetate dehalogenase]]
		+	[[Category: Rhodopseudomonas palustris]]
		+	[[Category: Chan, P W.Y.]]
		+	[[Category: Edwards, E A.]]
		+	[[Category: Pai, E F.]]
		+	[[Category: Yakunin, A F.]]

OCA at 07:48, 30 March 2011

2011-03-30T07:48:00Z

←Older revision		Revision as of 07:48, 30 March 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3r40 is ON HOLD	+	The entry 3r40 is ON HOLD until Paper Publication

	Authors: Chan, P.W.Y., Yakunin, A.F., Edwards, E.A., Pai, E.F.		Authors: Chan, P.W.Y., Yakunin, A.F., Edwards, E.A., Pai, E.F.

-	Description: Crystal Structure of the Fluoroacetate Dehalogenase ~~RPA116~~ -Asp110Asn/apo	+	Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 -Asp110Asn/apo

OCA: Protected "3r40" [edit=sysop:move=sysop]

2011-03-23T06:51:26Z

Protected "3r40" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:51, 23 March 2011

OCA: New page: '''Unreleased structure''' The entry 3r40 is ON HOLD Authors: Chan, P.W.Y., Yakunin, A.F., Edwards, E.A., Pai, E.F. Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA...

2011-03-23T06:51:25Z

New page: '''Unreleased structure''' The entry 3r40 is ON HOLD Authors: Chan, P.W.Y., Yakunin, A.F., Edwards, E.A., Pai, E.F. Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA...

New page

'''Unreleased structure'''

The entry 3r40 is ON HOLD

Authors: Chan, P.W.Y., Yakunin, A.F., Edwards, E.A., Pai, E.F.

Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA116 -Asp110Asn/apo