6qku - Revision history

OCA at 10:40, 15 November 2023

OCA — Wed, 15 Nov 2023 10:40:56 GMT

←Older revision		Revision as of 10:40, 15 November 2023
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	<StructureSection load='6qku' size='340' side='right'caption='[[6qku]], [[Resolution\|resolution]] 1.51Å' scene=''>		<StructureSection load='6qku' size='340' side='right'caption='[[6qku]], [[Resolution\|resolution]] 1.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qku]] 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=6QKU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QKU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qku]] 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=6QKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKU 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>, <scene name='pdbligand=R3W:CHLOROACETIC+ACID'>R3W</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]] 1.511Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D1920_22720 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1076 "Rhodobacillus palustris" Molisch 1907])</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>, <scene name='pdbligand=R3W:CHLOROACETIC+ACID'>R3W</scene></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=6qku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qku OCA], [~~http~~://pdbe.org/6qku PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qku RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qku PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qku 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=6qku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qku OCA], [https://pdbe.org/6qku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qku RCSB], [https://www.ebi.ac.uk/pdbsum/6qku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qku ProSAT]</span></td></tr>
	</table>		</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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6qku" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6qku" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Rhodobacillus palustris molisch 1907]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kim, T H~~]]	+	[[Category: Rhodopseudomonas palustris]]
-	[[Category: ~~Mehrabi, P~~]]	+	[[Category: Kim TH]]
-	[[Category: ~~Pai, E F~~]]	+	[[Category: Mehrabi P]]
-	[[Category: ~~Prosser, R S~~]]	+	[[Category: Pai EF]]
-	[[Category: ~~Allostery]]~~	+	[[Category: Prosser RS]]
-	~~[[Category: Dynamic]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolaser]]~~	+
-	~~[[Category: Substrate inhibition~~]]	+

OCA at 07:04, 31 July 2019

OCA — Wed, 31 Jul 2019 07:04:36 GMT

←Older revision		Revision as of 07:04, 31 July 2019
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	<StructureSection load='6qku' size='340' side='right'caption='[[6qku]], [[Resolution\|resolution]] 1.51Å' scene=''>		<StructureSection load='6qku' size='340' side='right'caption='[[6qku]], [[Resolution\|resolution]] 1.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qku]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qku]] 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=6QKU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKU 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>, <scene name='pdbligand=R3W:CHLOROACETIC+ACID'>R3W</scene></td></tr>		</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>, <scene name='pdbligand=R3W:CHLOROACETIC+ACID'>R3W</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">D1920_22720 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1076 "Rhodobacillus palustris" Molisch 1907])</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=6qku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qku OCA], [http://pdbe.org/6qku PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qku RCSB], [http://www.ebi.ac.uk/pdbsum/6qku PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qku ProSAT]</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=6qku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qku OCA], [http://pdbe.org/6qku PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qku RCSB], [http://www.ebi.ac.uk/pdbsum/6qku PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qku ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Rhodobacillus palustris molisch 1907]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kim, T H]]		[[Category: Kim, T H]]

OCA at 07:06, 26 June 2019

OCA — Wed, 26 Jun 2019 07:06:33 GMT

←Older revision		Revision as of 07:06, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qku is ~~ON HOLD~~	+	==Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Tyr219Phe - Chloroacetate soaked 2hr==
		+	<StructureSection load='6qku' size='340' side='right'caption='[[6qku]], [[Resolution\|resolution]] 1.51Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qku]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKU 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>, <scene name='pdbligand=R3W:CHLOROACETIC+ACID'>R3W</scene></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=6qku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qku OCA], [http://pdbe.org/6qku PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qku RCSB], [http://www.ebi.ac.uk/pdbsum/6qku PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qku ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an inter-protomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by NMR and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.

-	~~Authors: Mehrabi~~, P., Kim, ~~T.H.~~, ~~Prosser~~, R~~.S.~~, Pai, E.F.	+	Substrate-based Allosteric Regulation of a Homodimeric Enzyme.,Mehrabi P, Di Pietrantonio C, Kim TH, Sljoka A, Taverner K, Ing C, Kruglyak N, Pomes R, Pai EF, Prosser RS J Am Chem Soc. 2019 Jun 12. doi: 10.1021/jacs.9b03703. PMID:31188575<ref>PMID:31188575</ref>

-	~~Description: Crystal Structure~~ of the ~~Fluoroacetate Dehalogenase RPA1163~~ -~~Tyr219Phe~~ -~~Chloroacetate soaked 2hr~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Pai~~, ~~E.F~~]]	+	<div class="pdbe-citations 6qku" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kim, T H]]
	[[Category: Mehrabi, P]]		[[Category: Mehrabi, P]]
-	[[Category: Prosser, R.S]]	+	[[Category: Pai, E F]]
-	[[Category: ~~Kim, T.H~~]]	+	[[Category: Prosser, R S]]
		+	[[Category: Allostery]]
		+	[[Category: Dynamic]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolaser]]
		+	[[Category: Substrate inhibition]]

OCA: Protected "6qku" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 08:01:28 GMT

Protected "6qku" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:01, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qku is ON HOLD Authors: Mehrabi, P., Kim, T.H., Prosser, R.S., Pai, E.F. Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 ...

OCA — Wed, 13 Feb 2019 08:01:27 GMT

New page: '''Unreleased structure''' The entry 6qku is ON HOLD Authors: Mehrabi, P., Kim, T.H., Prosser, R.S., Pai, E.F. Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 ...

New page

'''Unreleased structure'''

The entry 6qku is ON HOLD

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

Description: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 -Tyr219Phe -Chloroacetate soaked 2hr
[[Category: Unreleased Structures]]
[[Category: Pai, E.F]]
[[Category: Mehrabi, P]]
[[Category: Prosser, R.S]]
[[Category: Kim, T.H]]