2abr - Revision history

OCA at 07:22, 23 August 2023

2023-08-23T07:22:15Z

←Older revision		Revision as of 07:22, 23 August 2023
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	<StructureSection load='2abr' size='340' side='right'caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2abr' size='340' side='right'caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ABR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ABR FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</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]] 2.9Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1rxx\|1rxx]]~~, [[~~2a9g~~\|~~2a9g~~]]~~, [[2aaf\|2aaf]], [[2aci\|2aci]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>arcA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~287~~ "~~Bacillus aeruginosus~~" ~~(Schroeter 1872) Trevisan 1885])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~https://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number~~ [~~https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6~~] </~~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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [https://pdbe.org/2abr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [https://www.ebi.ac.uk/pdbsum/2abr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2abr 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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [https://pdbe.org/2abr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [https://www.ebi.ac.uk/pdbsum/2abr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2abr ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ARCA_PSEAE ARCA_PSEAE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arginine deiminase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dunaway-Mariano, D]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: Galkin, A]]	+	[[Category: Dunaway-Mariano D]]
-	[[Category: Herzberg, O]]	+	[[Category: Galkin A]]
-	[[Category: Lu, X]]	+	[[Category: Herzberg O]]
-	~~[[Category: Arginine degradation pathway]]~~	+	[[Category: Lu X]]
-	~~[[Category: Catalytic mechanism]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: L-arginine deiminase~~]]	+

OCA at 08:29, 27 January 2021

2021-01-27T08:29:23Z

←Older revision		Revision as of 08:29, 27 January 2021
Line 1:		Line 1:

	==Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate==		==Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate==
-	<StructureSection load='2abr' size='340' side='right' caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='2abr' size='340' side='right'caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ABR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ABR FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rxx\|1rxx]], [[2a9g\|2a9g]], [[2aaf\|2aaf]], [[2aci\|2aci]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rxx\|1rxx]], [[2a9g\|2a9g]], [[2aaf\|2aaf]], [[2aci\|2aci]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [~~http~~://pdbe.org/2abr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2abr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2abr 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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [https://pdbe.org/2abr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [https://www.ebi.ac.uk/pdbsum/2abr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2abr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Arginine deiminase]]		[[Category: Arginine deiminase]]
		+	[[Category: Large Structures]]
	[[Category: Dunaway-Mariano, D]]		[[Category: Dunaway-Mariano, D]]
	[[Category: Galkin, A]]		[[Category: Galkin, A]]

OCA at 07:11, 9 May 2018

2018-05-09T07:11:01Z

←Older revision		Revision as of 07:11, 9 May 2018
Line 1:		Line 1:
		+
	==Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate==		==Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate==
	<StructureSection load='2abr' size='340' side='right' caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2abr' size='340' side='right' caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [http://pdbe.org/2abr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [http://www.ebi.ac.uk/pdbsum/2abr 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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [http://pdbe.org/2abr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [http://www.ebi.ac.uk/pdbsum/2abr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2abr 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/ab/2abr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ab/2abr_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>
	</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=2abr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:22, 11 September 2015

2015-09-11T09:22:15Z

←Older revision		Revision as of 09:22, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2abr' size='340' side='right' caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='2abr' size='340' side='right' caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa Pseudomonas aeruginosa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ABR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ABR FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rxx\|1rxx]], [[2a9g\|2a9g]], [[2aaf\|2aaf]], [[2aci\|2aci]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rxx\|1rxx]], [[2a9g\|2a9g]], [[2aaf\|2aaf]], [[2aci\|2aci]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 ~~Pseudomonas aeruginosa~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [http://www.ebi.ac.uk/pdbsum/2abr 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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [http://pdbe.org/2abr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [http://www.ebi.ac.uk/pdbsum/2abr 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 2abr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Arginine deiminase]]		[[Category: Arginine deiminase]]
-	[[Category: Pseudomonas aeruginosa]]
	[[Category: Dunaway-Mariano, D]]		[[Category: Dunaway-Mariano, D]]
	[[Category: Galkin, A]]		[[Category: Galkin, A]]

OCA at 09:31, 8 January 2015

2015-01-08T09:31:36Z

←Older revision		Revision as of 09:31, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ABR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ABR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rxx\|1rxx]], [[2a9g\|2a9g]], [[2aaf\|2aaf]], [[2aci\|2aci]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rxx\|1rxx]], [[2a9g\|2a9g]], [[2aaf\|2aaf]], [[2aci\|2aci]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [http://www.ebi.ac.uk/pdbsum/2abr 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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [http://www.ebi.ac.uk/pdbsum/2abr 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 33:		Line 33:
	[[Category: Arginine deiminase]]		[[Category: Arginine deiminase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: Dunaway-Mariano, D.]]	+	[[Category: Dunaway-Mariano, D]]
-	[[Category: Galkin, A.]]	+	[[Category: Galkin, A]]
-	[[Category: Herzberg, O.]]	+	[[Category: Herzberg, O]]
-	[[Category: Lu, X.]]	+	[[Category: Lu, X]]
	[[Category: Arginine degradation pathway]]		[[Category: Arginine degradation pathway]]
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: L-arginine deiminase]]		[[Category: L-arginine deiminase]]

OCA at 01:59, 30 September 2014

2014-09-30T01:59:54Z

←Older revision		Revision as of 01:59, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2abr.~~png~~\|~~left~~\|200px]]	+	==Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate==
		+	<StructureSection load='2abr' size='340' side='right' caption='[[2abr]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2abr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ABR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYR:N~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE'>CYR</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rxx\|1rxx]], [[2a9g\|2a9g]], [[2aaf\|2aaf]], [[2aci\|2aci]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">arcA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_deiminase Arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.6 3.5.3.6] </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=2abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2abr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2abr RCSB], [http://www.ebi.ac.uk/pdbsum/2abr 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/ab/2abr_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 ==
		+	L-arginine deiminase (ADI) catalyzes the irreversible hydrolysis of L-arginine to citrulline and ammonia. In a previous report of the structure of apoADI from Pseudomonas aeruginosa, the four residues that form the catalytic motif were identified as Cys406, His278, Asp280, and Asp166. The function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. In this study, the structure of the C406A mutant in complex with L-arginine is reported to provide a snapshot of the enzyme.substrate complex. Through the comparison of the structures of apoenzyme and substrate-bound enzyme, a substrate-induced conformational transition, which might play an important role in activity regulation, was discovered. Furthermore, the position of the guanidinium group of the bound substrate relative to the side chains of His278, Asp280, and Asp166 indicated that these residues mediate multiple proton transfers. His278 and Asp280, which are positioned to activate the water nucleophile in the hydrolysis of the S-alkylthiouronium intermediate, were replaced with alanine to stabilize the intermediate for structure determination. The structures determined for the H278A and D280A mutants co-crystallized with L-arginine provide a snapshot of the S-alkylthiouronium adduct formed by attack of Cys406 on the guanidinium carbon of L-arginine followed by the elimination of ammonia. Asp280 and Asp166 engage in ionic interactions with the guanidinium group in the C406A ADI. L-arginine structure and might orient the reaction center and participate in proton transfer. Structure determination of D166A revealed the apoD166A ADI. The collection of structures is interpreted in the context of recent biochemical data to propose a model for ADI substrate recognition and catalysis.

-	~~{{STRUCTURE_2abr\| PDB=2abr \| SCENE= }}~~	+	Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase.,Galkin A, Lu X, Dunaway-Mariano D, Herzberg O J Biol Chem. 2005 Oct 7;280(40):34080-7. Epub 2005 Aug 9. PMID:16091358<ref>PMID:16091358</ref>

-	~~===Structure~~ of ~~D280A arginine deiminase with L-arginine forming a~~ S~~-alkylthiouronium reaction intermediate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16091358}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2abr]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016091358<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Arginine deiminase]]		[[Category: Arginine deiminase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]

OCA: Protected "2abr" [edit=sysop:move=sysop]

2013-01-06T11:13:27Z

Protected "2abr" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:13, 6 January 2013

OCA at 11:13, 6 January 2013

2013-01-06T11:13:25Z

←Older revision		Revision as of 11:13, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2abr.png\|left\|200px]]		[[Image:2abr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2abr", 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_2abr\| PDB=2abr \| SCENE= }}		{{STRUCTURE_2abr\| PDB=2abr \| SCENE= }}

	===Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate===		===Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16091358}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16091358 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16091358}}		{{ABSTRACT_PUBMED_16091358}}

	==About this Structure==		==About this Structure==
-	~~2ABR~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA].	+	[[2abr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16091358~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016091358</ref><references group="xtra"/>
	[[Category: Arginine deiminase]]		[[Category: Arginine deiminase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
Line 32:		Line 20:
	[[Category: Arginine degradation pathway]]		[[Category: Arginine degradation pathway]]
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]
		+	[[Category: Hydrolase]]
	[[Category: L-arginine deiminase]]		[[Category: L-arginine deiminase]]
-	[[Category: X-ray structure]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:40:24 2009''

OCA at 16:40, 17 February 2009

2009-02-17T16:40:26Z

←Older revision		Revision as of 16:40, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2ABR is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA].	+	2ABR is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ABR OCA].

	==Reference==		==Reference==
-	Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase., Galkin A, Lu X, Dunaway-Mariano D, Herzberg O, J Biol Chem. 2005 Oct 7;280(40):34080-7. Epub 2005 Aug 9. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16091358 16091358]~~	+	<ref group="xtra">PMID:16091358</ref><references group="xtra"/>
	[[Category: Arginine deiminase]]		[[Category: Arginine deiminase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: Single protein]]
	[[Category: Dunaway-Mariano, D.]]		[[Category: Dunaway-Mariano, D.]]
	[[Category: Galkin, A.]]		[[Category: Galkin, A.]]
Line 36:		Line 35:
	[[Category: X-ray structure]]		[[Category: X-ray structure]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:40:~~37 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:40:24 2009''

OCA at 23:40, 28 July 2008

2008-07-28T23:40:43Z

←Older revision		Revision as of 23:40, 28 July 2008
Line 1:		Line 1:
-	[[Image:2abr.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2abr.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2abr\| PDB=2abr \| SCENE= }}		{{STRUCTURE_2abr\| PDB=2abr \| SCENE= }}

-	~~'''~~Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate~~'''~~	+	===Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate===


-	~~==Overview==~~	+	<!--
-	L-~~arginine deiminase (ADI) catalyzes the irreversible hydrolysis of L~~-arginine to citrulline and ammonia. In a previous report of the structure of apoADI from Pseudomonas aeruginosa, the four residues that form the catalytic motif were identified as Cys406, His278, Asp280, and Asp166. The ~~function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. In~~ this ~~study~~, the ~~structure of the C406A mutant in complex with L-arginine is reported~~ to ~~provide a snapshot of~~ the ~~enzyme~~.~~substrate complex~~. Through the comparison of the structures of apoenzyme and substrate-bound enzyme, a substrate-induced conformational transition, which might play an important role in activity regulation, was discovered. Furthermore, the ~~position of the guanidinium group of the bound substrate relative to the side chains of His278, Asp280, and Asp166 indicated that these residues mediate multiple proton transfers~~. ~~His278 and Asp280, which are positioned to activate the water nucleophile in the hydrolysis of the S~~-~~alkylthiouronium intermediate, were replaced with alanine to stabilize the intermediate for structure determination. The structures determined for the H278A and D280A mutants co~~-crystallized with L-arginine provide a snapshot of the S-alkylthiouronium adduct formed by attack of Cys406 on the guanidinium carbon of L-arginine followed by the elimination of ammonia. Asp280 and Asp166 engage in ionic interactions with the guanidinium group in the C406A ADI. L-arginine structure and might orient the reaction center and participate in proton transfer. Structure determination of D166A revealed the apoD166A ADI. The collection of structures is interpreted in the context of recent biochemical data to propose a model for ADI substrate recognition and catalysis.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16091358}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16091358 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16091358}}

	==About this Structure==		==About this Structure==
Line 31:		Line 35:
	[[Category: L-arginine deiminase]]		[[Category: L-arginine deiminase]]
	[[Category: X-ray structure]]		[[Category: X-ray structure]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 18~~:51:25 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:40:37 2008''