1ejs - Revision history

OCA at 10:03, 20 March 2024

2024-03-20T10:03:16Z

←Older revision		Revision as of 10:03, 20 March 2024
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	<StructureSection load='1ejs' size='340' side='right'caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1ejs' size='340' side='right'caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EJS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ejr\|1ejr]]~~, ~~[[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Urease Urease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5]~~ </~~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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [https://pdbe.org/1ejs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [https://www.ebi.ac.uk/pdbsum/1ejs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejs 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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [https://pdbe.org/1ejs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [https://www.ebi.ac.uk/pdbsum/1ejs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejs ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/URE1_KLEAE URE1_KLEAE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ejs ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ejs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Klebsiella aerogenes urease uses a dinuclear nickel active site to catalyze urea hydrolysis at >10(14)-fold the spontaneous rate. To better define the enzyme mechanism, we examined the kinetics and structures for a suite of site-directed variants involving four residues at the active site: His320, His219, Asp221, and Arg336. Compared to wild-type urease, the H320A, H320N, and H320Q variants exhibit similar approximately 10(-)(5)-fold deficiencies in rates, modest K(m) changes, and disorders in the peptide flap covering their active sites. The pH profiles for these mutant enzymes are anomalous with optima near 6 and shoulders that extend to pH 9. H219A urease exhibits 10(3)-fold increased K(m) over that of native enzyme, whereas the increase is less marked ( approximately 10(2)-fold) in the H219N and H219Q variants that retain hydrogen bonding capability. Structures for these variants show clearly resolved active site water molecules covered by well-ordered peptide flaps. Whereas the D221N variant is only moderately affected compared to wild-type enzyme, D221A urease possesses low activity ( approximately 10(-)(3) that of native enzyme), a small increase in K(m), and a pH 5 optimum. The crystal structure for D221A urease is reminiscent of the His320 variants. The R336Q enzyme has a approximately 10(-)(4)-fold decreased catalytic rate with near-normal pH dependence and an unaffected K(m). Phenylglyoxal inactivates the R336Q variant at over half the rate observed for native enzyme, demonstrating that modification of non-active-site arginines can eliminate activity, perhaps by affecting the peptide flap. Our data favor a mechanism in which His219 helps to polarize the substrate carbonyl group, a metal-bound terminal hydroxide or bridging oxo-dianion attacks urea to form a tetrahedral intermediate, and protonation occurs via the general acid His320 with Asp221 and Arg336 orienting and influencing the acidity of this residue. Furthermore, we conclude that the simple bell-shaped pH dependence of k(cat) and k(cat)/K(m) for the native enzyme masks a more complex underlying pH dependence involving at least four pK(a)s.
-
-	Kinetic and structural characterization of urease active site variants.,Pearson MA, Park IS, Schaller RA, Michel LO, Karplus PA, Hausinger RP Biochemistry. 2000 Jul 25;39(29):8575-84. PMID:10913264<ref>PMID:10913264</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ejs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Urease 3D structures\|Urease 3D structures]]		*[[Urease 3D structures\|Urease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Klebsiella aerogenes]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Urease]]~~	+	[[Category: Hausinger RP]]
-	[[Category: Hausinger~~, R P~~]]	+	[[Category: Karplus PA]]
-	[[Category: Karplus~~, P A~~]]	+	[[Category: Michel LO]]
-	[[Category: Michel~~, L O~~]]	+	[[Category: Park IS]]
-	[[Category: Park~~, I S~~]]	+	[[Category: Pearson MA]]
-	[[Category: Pearson~~, M A~~]]	+	[[Category: Schaller RA]]
-	[[Category: Schaller~~, R A]]~~	+
-	~~[[Category: Alpha-beta barrel]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nickel metalloenzyme~~]]	+

OCA at 09:38, 21 July 2021

2021-07-21T09:38:30Z

←Older revision		Revision as of 09:38, 21 July 2021
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	<StructureSection load='1ejs' size='340' side='right'caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1ejs' size='340' side='right'caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EJS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Urease Urease], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Urease Urease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [~~http~~://pdbe.org/1ejs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ejs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejs 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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [https://pdbe.org/1ejs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [https://www.ebi.ac.uk/pdbsum/1ejs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejs ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Urease\|Urease]]	+	*[[Urease 3D structures\|Urease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:38, 16 October 2019

2019-10-16T14:38:49Z

←Older revision		Revision as of 14:38, 16 October 2019
Line 1:		Line 1:

	==Crystal Structure of the H219N Variant of Klebsiella Aerogenes Urease==		==Crystal Structure of the H219N Variant of Klebsiella Aerogenes Urease==
-	<StructureSection load='1ejs' size='340' side='right' caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1ejs' size='340' side='right'caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EJS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EJS FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1ejs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ejs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Urease\|Urease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Urease]]		[[Category: Urease]]
	[[Category: Hausinger, R P]]		[[Category: Hausinger, R P]]

OCA at 07:20, 20 December 2017

2017-12-20T07:20:34Z

←Older revision		Revision as of 07:20, 20 December 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the H219N Variant of Klebsiella Aerogenes Urease==		==Crystal Structure of the H219N Variant of Klebsiella Aerogenes Urease==
	<StructureSection load='1ejs' size='340' side='right' caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1ejs' size='340' side='right' caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [http://pdbe.org/1ejs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [http://www.ebi.ac.uk/pdbsum/1ejs 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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [http://pdbe.org/1ejs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [http://www.ebi.ac.uk/pdbsum/1ejs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ejs ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ej/1ejs_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ej/1ejs_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 1ejs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ejs" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Urease\|Urease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:09, 10 February 2016

2016-02-10T07:09:29Z

←Older revision		Revision as of 07:09, 10 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ejs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:33, 11 September 2015

2015-09-11T06:33:19Z

←Older revision		Revision as of 06:33, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ejs' size='340' side='right' caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1ejs' size='340' side='right' caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EJS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [http://www.ebi.ac.uk/pdbsum/1ejs 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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [http://pdbe.org/1ejs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [http://www.ebi.ac.uk/pdbsum/1ejs PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 1ejs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Enterobacter aerogenes]]
	[[Category: Urease]]		[[Category: Urease]]
	[[Category: Hausinger, R P]]		[[Category: Hausinger, R P]]

OCA at 20:49, 22 December 2014

2014-12-22T20:49:55Z

←Older revision		Revision as of 20:49, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EJS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EJS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [http://www.ebi.ac.uk/pdbsum/1ejs 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=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [http://www.ebi.ac.uk/pdbsum/1ejs PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Enterobacter aerogenes]]		[[Category: Enterobacter aerogenes]]
	[[Category: Urease]]		[[Category: Urease]]
-	[[Category: Hausinger, R P.]]	+	[[Category: Hausinger, R P]]
-	[[Category: Karplus, P A.]]	+	[[Category: Karplus, P A]]
-	[[Category: Michel, L O.]]	+	[[Category: Michel, L O]]
-	[[Category: Park, I S.]]	+	[[Category: Park, I S]]
-	[[Category: Pearson, M A.]]	+	[[Category: Pearson, M A]]
-	[[Category: Schaller, R A.]]	+	[[Category: Schaller, R A]]
	[[Category: Alpha-beta barrel]]		[[Category: Alpha-beta barrel]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nickel metalloenzyme]]		[[Category: Nickel metalloenzyme]]

OCA at 11:30, 24 September 2014

2014-09-24T11:30:10Z

←Older revision		Revision as of 11:30, 24 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ejs.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the H219N Variant of Klebsiella Aerogenes Urease==
		+	<StructureSection load='1ejs' size='340' side='right' caption='[[1ejs]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ejs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EJS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
		+	<tr><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ejr\|1ejr]], [[1ejt\|1ejt]], [[1eju\|1eju]], [[1ejv\|1ejv]], [[1ejw\|1ejw]], [[1ejx\|1ejx]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ejs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ejs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ejs RCSB], [http://www.ebi.ac.uk/pdbsum/1ejs PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ej/1ejs_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Klebsiella aerogenes urease uses a dinuclear nickel active site to catalyze urea hydrolysis at >10(14)-fold the spontaneous rate. To better define the enzyme mechanism, we examined the kinetics and structures for a suite of site-directed variants involving four residues at the active site: His320, His219, Asp221, and Arg336. Compared to wild-type urease, the H320A, H320N, and H320Q variants exhibit similar approximately 10(-)(5)-fold deficiencies in rates, modest K(m) changes, and disorders in the peptide flap covering their active sites. The pH profiles for these mutant enzymes are anomalous with optima near 6 and shoulders that extend to pH 9. H219A urease exhibits 10(3)-fold increased K(m) over that of native enzyme, whereas the increase is less marked ( approximately 10(2)-fold) in the H219N and H219Q variants that retain hydrogen bonding capability. Structures for these variants show clearly resolved active site water molecules covered by well-ordered peptide flaps. Whereas the D221N variant is only moderately affected compared to wild-type enzyme, D221A urease possesses low activity ( approximately 10(-)(3) that of native enzyme), a small increase in K(m), and a pH 5 optimum. The crystal structure for D221A urease is reminiscent of the His320 variants. The R336Q enzyme has a approximately 10(-)(4)-fold decreased catalytic rate with near-normal pH dependence and an unaffected K(m). Phenylglyoxal inactivates the R336Q variant at over half the rate observed for native enzyme, demonstrating that modification of non-active-site arginines can eliminate activity, perhaps by affecting the peptide flap. Our data favor a mechanism in which His219 helps to polarize the substrate carbonyl group, a metal-bound terminal hydroxide or bridging oxo-dianion attacks urea to form a tetrahedral intermediate, and protonation occurs via the general acid His320 with Asp221 and Arg336 orienting and influencing the acidity of this residue. Furthermore, we conclude that the simple bell-shaped pH dependence of k(cat) and k(cat)/K(m) for the native enzyme masks a more complex underlying pH dependence involving at least four pK(a)s.

-	~~{{STRUCTURE_1ejs\| PDB=1ejs \| SCENE= }}~~	+	Kinetic and structural characterization of urease active site variants.,Pearson MA, Park IS, Schaller RA, Michel LO, Karplus PA, Hausinger RP Biochemistry. 2000 Jul 25;39(29):8575-84. PMID:10913264<ref>PMID:10913264</ref>

-	~~===Crystal Structure~~ of the ~~H219N Variant of Klebsiella Aerogenes Urease===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10913264}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ejs]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA].~~	+

	==See Also==		==See Also==
	*[[Urease\|Urease]]		*[[Urease\|Urease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010913264<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacter aerogenes]]		[[Category: Enterobacter aerogenes]]
	[[Category: Urease]]		[[Category: Urease]]

OCA at 16:46, 20 October 2012

2012-10-20T16:46:03Z

←Older revision		Revision as of 16:46, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ejs]] is a 3 chain structure ~~of [[Urease]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA].	+	[[1ejs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EJS OCA].

	==See Also==		==See Also==

OCA: Protected "1ejs" [edit=sysop:move=sysop]

2012-07-26T22:46:22Z

Protected "1ejs" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:46, 26 July 2012