5k3c - Revision history

OCA at 09:51, 27 September 2023

OCA — Wed, 27 Sep 2023 09:51:08 GMT

←Older revision		Revision as of 09:51, 27 September 2023
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	<StructureSection load='5k3c' size='340' side='right'caption='[[5k3c]], [[Resolution\|resolution]] 1.54Å' scene=''>		<StructureSection load='5k3c' size='340' side='right'caption='[[5k3c]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3c]] 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=5K3C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K3C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_CGA009 Rhodopseudomonas palustris CGA009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K3C FirstGlance]. <br>
-	</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></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]] 1.541Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>~~[[~~Non-Standard_Residue~~\|~~NonStd Res:~~]]~~</b></td><td class="sblockDat"><scene name='pdbligand=FTR:FLUOROTRYPTOPHANE'>FTR</scene>~~</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=FTR:FLUOROTRYPTOPHANE'>FTR</scene></td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5k3b\|5k3b]], [[5k3a\|5k3a]], [[5k3d\|5k3d]], [[5k3f\|5k3f]], [[5k3e\|5k3e]]</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=5k3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3c OCA], [https://pdbe.org/5k3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k3c RCSB], [https://www.ebi.ac.uk/pdbsum/5k3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3c ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5k3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3c OCA], [~~http~~://pdbe.org/5k3c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k3c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k3c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3c 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Haloacetate dehalogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rhopa~~]]	+	[[Category: Rhodopseudomonas palustris CGA009]]
-	[[Category: Kim~~, T H~~]]	+	[[Category: Kim TH]]
-	[[Category: Mehrabi, P]]	+	[[Category: Mehrabi P]]
-	[[Category: Pai~~, E F~~]]	+	[[Category: Pai EF]]
-	[[Category: Prosser~~, S R]]~~	+	[[Category: Prosser SR]]
-	~~[[Category: Dehalogenase]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:17, 25 June 2020

OCA — Thu, 25 Jun 2020 09:17:14 GMT

←Older revision		Revision as of 09:17, 25 June 2020
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	==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/5-Fluorotryptophan==		==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/5-Fluorotryptophan==
-	<StructureSection load='5k3c' size='340' side='right' caption='[[5k3c]], [[Resolution\|resolution]] 1.54Å' scene=''>	+	<StructureSection load='5k3c' size='340' side='right'caption='[[5k3c]], [[Resolution\|resolution]] 1.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3c]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3C OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K3C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3c]] 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=5K3C OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K3C 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></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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FTR:FLUOROTRYPTOPHANE'>FTR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FTR:FLUOROTRYPTOPHANE'>FTR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3b\|5k3b]], [[5k3a\|5k3a]], [[5k3d\|5k3d]], [[5k3f\|5k3f]], [[5k3e\|5k3e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3b\|5k3b]], [[5k3a\|5k3a]], [[5k3d\|5k3d]], [[5k3f\|5k3f]], [[5k3e\|5k3e]]</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://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5k3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3c OCA], [http://pdbe.org/5k3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3c RCSB], [http://www.ebi.ac.uk/pdbsum/5k3c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3c ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3c OCA], [http://pdbe.org/5k3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3c RCSB], [http://www.ebi.ac.uk/pdbsum/5k3c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5k3c" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k3c" 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]]

OCA at 17:55, 1 February 2017

OCA — Wed, 01 Feb 2017 17:55:27 GMT

←Older revision		Revision as of 17:55, 1 February 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5k3c is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/5-Fluorotryptophan==
		+	<StructureSection load='5k3c' size='340' side='right' caption='[[5k3c]], [[Resolution\|resolution]] 1.54Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k3c]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3C 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></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FTR:FLUOROTRYPTOPHANE'>FTR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3b\|5k3b]], [[5k3a\|5k3a]], [[5k3d\|5k3d]], [[5k3f\|5k3f]], [[5k3e\|5k3e]]</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=5k3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3c OCA], [http://pdbe.org/5k3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3c RCSB], [http://www.ebi.ac.uk/pdbsum/5k3c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3c ProSAT]</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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Freeze-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.

-	~~Authors: Mehrabi, P~~., Kim, ~~T.H.~~, ~~Prosser~~, S.R., ~~Pai~~, E.F.	+	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<ref>PMID:28104837</ref>

-	~~Description: Crystal Structure~~ of the ~~Fluoroacetate Dehalogenase RPA1163 -WT~~/~~5-Fluorotryptophan~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Prosser, S.R~~]]	+	<div class="pdbe-citations 5k3c" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Pai~~, ~~E.F~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Haloacetate dehalogenase]]
		+	[[Category: Kim, T H]]
	[[Category: Mehrabi, P]]		[[Category: Mehrabi, P]]
-	[[Category: ~~Kim~~, ~~T.H~~]]	+	[[Category: Pai, E F]]
		+	[[Category: Prosser, S R]]
		+	[[Category: Dehalogenase]]
		+	[[Category: Homodimer]]
		+	[[Category: Hydrolase]]

OCA at 13:23, 20 June 2016

OCA — Mon, 20 Jun 2016 13:23:44 GMT

←Older revision		Revision as of 13:23, 20 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k3c is ON HOLD	+	The entry 5k3c is ON HOLD until Paper Publication

	Authors: Mehrabi, P., Kim, T.H., Prosser, S.R., Pai, E.F.		Authors: Mehrabi, P., Kim, T.H., Prosser, S.R., Pai, E.F.

OCA: Protected "5k3c" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:16:05 GMT

Protected "5k3c" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:16, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k3c is ON HOLD Authors: Mehrabi, P., Kim, T.H., Prosser, S.R., Pai, E.F. Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 ...

OCA — Wed, 01 Jun 2016 14:16:04 GMT

New page: '''Unreleased structure''' The entry 5k3c is ON HOLD Authors: Mehrabi, P., Kim, T.H., Prosser, S.R., Pai, E.F. Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 ...

New page

'''Unreleased structure'''

The entry 5k3c is ON HOLD

Authors: Mehrabi, P., Kim, T.H., Prosser, S.R., Pai, E.F.

Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 -WT/5-Fluorotryptophan
[[Category: Unreleased Structures]]
[[Category: Prosser, S.R]]
[[Category: Pai, E.F]]
[[Category: Mehrabi, P]]
[[Category: Kim, T.H]]