4h9u - Revision history

OCA at 08:06, 3 November 2022

2022-11-03T08:06:31Z

←Older revision		Revision as of 08:06, 3 November 2022
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	==Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+==		==Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+==
-	<StructureSection load='4h9u' size='340' side='right' caption='[[4h9u]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4h9u' size='340' side='right'caption='[[4h9u]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h9u]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Geoka Geoka~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H9U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h9u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H9U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:~~HYDROXIDE~~+~~ION~~'>OH</scene>, <scene name='pdbligand=ZN:~~ZINC~~+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~KCX~~:~~LYSINE~~+~~NZ-CARBOXYLIC+ACID~~'>~~KCX~~</scene>~~</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=4h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h9u OCA], [https://pdbe.org/4h9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h9u RCSB], [https://www.ebi.ac.uk/pdbsum/4h9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h9u ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h9t\|4h9t]], [[4h9v\|4h9v]], [[4h9x\|4h9x]], [[4h9y\|4h9y]], [[4h9z\|4h9z]], [[4ha0\|4ha0]]</td></tr>	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1506 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])~~</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=4h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h9u OCA], [~~http~~://pdbe.org/4h9u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h9u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h9u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h9u ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5KZU5_GEOKA Q5KZU5_GEOKA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Phosphotriesterase\|Phosphotriesterase]]	+	*[[Phosphotriesterase 3D structures\|Phosphotriesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geoka~~]]	+	[[Category: Geobacillus kaustophilus HTA426]]
-	[[Category: ~~Chow, J Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Robinson, R C~~]]	+	[[Category: Chow JY]]
-	[[Category: ~~Xue, B~~]]	+	[[Category: Robinson RC]]
-	[[Category: ~~Yew, W S~~]]	+	[[Category: Xue B]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: Yew WS]]

OCA at 22:08, 4 August 2016

2016-08-04T22:08:48Z

←Older revision		Revision as of 22:08, 4 August 2016
Line 1:		Line 1:
		+
	==Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+==		==Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+==
	<StructureSection load='4h9u' size='340' side='right' caption='[[4h9u]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4h9u' size='340' side='right' caption='[[4h9u]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h9u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H9U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h9u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H9U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h9t\|4h9t]], [[4h9v\|4h9v]], [[4h9x\|4h9x]], [[4h9y\|4h9y]], [[4h9z\|4h9z]], [[4ha0\|4ha0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h9t\|4h9t]], [[4h9v\|4h9v]], [[4h9x\|4h9x]], [[4h9y\|4h9y]], [[4h9z\|4h9z]], [[4ha0\|4ha0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1506 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 ~~Geobacillus kaustophilus HTA426~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1506 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</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=4h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h9u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h9u RCSB], [http://www.ebi.ac.uk/pdbsum/4h9u 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=4h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h9u OCA], [http://pdbe.org/4h9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h9u RCSB], [http://www.ebi.ac.uk/pdbsum/4h9u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h9u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4h9u" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geobacillus kaustophilus hta426~~]]	+	[[Category: Geoka]]
	[[Category: Chow, J Y]]		[[Category: Chow, J Y]]
	[[Category: Robinson, R C]]		[[Category: Robinson, R C]]

OCA at 11:32, 21 December 2014

2014-12-21T11:32:49Z

←Older revision		Revision as of 11:32, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4h9u\| PDB=4h9u \| SCENE= }}~~	+	==Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+==
-	===Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+===	+	<StructureSection load='4h9u' size='340' side='right' caption='[[4h9u]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23461395}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4h9u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H9U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h9t\|4h9t]], [[4h9v\|4h9v]], [[4h9x\|4h9x]], [[4h9y\|4h9y]], [[4h9z\|4h9z]], [[4ha0\|4ha0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GK1506 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 Geobacillus kaustophilus HTA426])</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=4h9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h9u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h9u RCSB], [http://www.ebi.ac.uk/pdbsum/4h9u PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The in vitro evolution and engineering of quorum-quenching lactonases with enhanced reactivities was achieved using a thermostable GKL enzyme as a template, yielding the E101G/R230C GKL mutant with increased catalytic activity and a broadened substrate range [Chow, J. Y., Xue, B., Lee, K. H., Tung, A., Wu, L., Robinson, R. C., and Yew, W. S. (2010) J. Biol. Chem. 285, 40911-40920]. This enzyme possesses the (beta/alpha)8-barrel fold and is a member of the PLL (phosphotriesterase-like lactonase) group of enzymes within the amidohydrolase superfamily that hydrolyze N-acyl-homoserine lactones, which mediate the quorum-sensing pathways of bacteria. The structure of the evolved N-butyryl-l-homoserine lactone (substrate)-bound E101G/R230C GKL enzyme was determined, in the presence of the inactivating D266N mutation, to a resolution of 2.2 A to provide an explanation for the observed rate enhancements. In addition, the substrate-bound structure of the catalytically inactive E101N/D266N mutant of the manganese-reconstituted enzyme was determined to a resolution of 2.1 A and the structure of the ligand-free, manganese-reconstituted E101N mutant to a resolution of 2.6 A, and the structures of ligand-free zinc-reconstituted wild-type, E101N, R230D, and E101G/R230C mutants of GKL were determined to resolutions of 2.1, 2.1, 1.9, and 2.0 A, respectively. In particular, the structure of the evolved E101G/R230C mutant of GKL provides evidence of a catalytically productive active site architecture that contributes to the observed enhancement of catalysis. At high concentrations, wild-type and mutant GKL enzymes are differentially colored, with absorbance maxima in the range of 512-553 nm. The structures of the wild-type and mutant GKL provide a tractable link between the origins of the coloration and the charge-transfer complex between the alpha-cation and Tyr99 within the enzyme active site. Taken together, this study provides evidence of the modulability of enzymatic catalysis through subtle changes in enzyme active site architecture.

-	~~==About this Structure==~~	+	Structural evidence of a productive active site architecture for an evolved quorum-quenching GKL lactonase.,Xue B, Chow JY, Baldansuren A, Yap LL, Gan YH, Dikanov SA, Robinson RC, Yew WS Biochemistry. 2013 Apr 2;52(13):2359-70. doi: 10.1021/bi4000904. Epub 2013 Mar, 19. PMID:23461395<ref>PMID:23461395</ref>
-	~~[[4h9u]] is~~ a 2 ~~chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:023461395</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Phosphotriesterase\|Phosphotriesterase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Geobacillus kaustophilus hta426]]		[[Category: Geobacillus kaustophilus hta426]]
-	[[Category: Chow, J Y.]]	+	[[Category: Chow, J Y]]
-	[[Category: Robinson, R C.]]	+	[[Category: Robinson, R C]]
-	[[Category: Xue, B.]]	+	[[Category: Xue, B]]
-	[[Category: Yew, W S.]]	+	[[Category: Yew, W S]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 17:55, 19 June 2013

2013-06-19T17:55:36Z

←Older revision		Revision as of 17:55, 19 June 2013
Line 1:		Line 1:
-	[[Image:4h9u.jpg\|left\|200px]]
-
	{{STRUCTURE_4h9u\| PDB=4h9u \| SCENE= }}		{{STRUCTURE_4h9u\| PDB=4h9u \| SCENE= }}
-
	===Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+===		===Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+===
-		+	{{ABSTRACT_PUBMED_23461395}}

	==About this Structure==		==About this Structure==
	[[4h9u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA].		[[4h9u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023461395</ref><references group="xtra"/><references/>
	[[Category: Geobacillus kaustophilus hta426]]		[[Category: Geobacillus kaustophilus hta426]]
	[[Category: Chow, J Y.]]		[[Category: Chow, J Y.]]

OCA at 13:52, 8 November 2012

2012-11-08T13:52:39Z

←Older revision		Revision as of 13:52, 8 November 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4h9u.jpg\|left\|200px]]

-	~~The entry~~ 4h9u ~~is ON HOLD~~	+	{{STRUCTURE_4h9u\| PDB=4h9u \| SCENE= }}

-	~~Authors: Xue~~, ~~B., Chow, J.Y., Yew, W.S., Robinson, R.C.~~	+	===Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+===

-	~~Description:~~ Structure of Geobacillus kaustophilus ~~lactonase, wild~~-~~type with Zn2+~~	+
		+	==About this Structure==
		+	[[4h9u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus_hta426 Geobacillus kaustophilus hta426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H9U OCA].
		+	[[Category: Geobacillus kaustophilus hta426]]
		+	[[Category: Chow, J Y.]]
		+	[[Category: Robinson, R C.]]
		+	[[Category: Xue, B.]]
		+	[[Category: Yew, W S.]]
		+	[[Category: Hydrolase]]

OCA: Protected "4h9u" [edit=sysop:move=sysop]

2012-10-03T05:50:55Z

Protected "4h9u" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:50, 3 October 2012

OCA: New page: '''Unreleased structure''' The entry 4h9u is ON HOLD Authors: Xue, B., Chow, J.Y., Yew, W.S., Robinson, R.C. Description: Structure of Geobacillus kaustophilus lactonase, wild-type wit...

2012-10-03T05:50:54Z

New page: '''Unreleased structure''' The entry 4h9u is ON HOLD Authors: Xue, B., Chow, J.Y., Yew, W.S., Robinson, R.C. Description: Structure of Geobacillus kaustophilus lactonase, wild-type wit...

New page

'''Unreleased structure'''

The entry 4h9u is ON HOLD

Authors: Xue, B., Chow, J.Y., Yew, W.S., Robinson, R.C.

Description: Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+