2jer - Revision history

OCA at 14:45, 13 December 2023

2023-12-13T14:45:35Z

← Older revision		Revision as of 14:45, 13 December 2023
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	<StructureSection load='2jer' size='340' side='right'caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2jer' size='340' side='right'caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JER FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JER FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=AGT:S~~-~~{(S)-AMINO~~[~~(4-AMINOBUTYL)AMINO~~]~~METHYL}-L-CYSTEINE'>AGT</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]] 1.65Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2j2t\|2j2t]]</div></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</scene></td></tr>
	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number~~ [~~https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12~~] </~~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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [https://pdbe.org/2jer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [https://www.ebi.ac.uk/pdbsum/2jer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer 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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [https://pdbe.org/2jer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [https://www.ebi.ac.uk/pdbsum/2jer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/AGUA_ENTFA AGUA_ENTFA]
	== 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: Enterococcus ~~proteiformis thiercelin and jouhaud 1903]]~~		[[Category: Enterococcus faecalis]]
	~~[[Category: Agmatine deiminase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Llacer~~, J L~~]]		[[Category: Llacer JL]]
	[[Category: Rubio, V]]		[[Category: Rubio V]]
	[[Category: Tavarez, S]]		[[Category: Tavarez S]]
	~~[[Category: 5- fold pseudosymmetric structure]]~~
	~~[[Category: Agdi]]~~
	~~[[Category: Agmatine degradation pathway]]~~
	~~[[Category: Agmatine iminohydrolase]]~~
	~~[[Category: Covalent amidino adduct]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Tetramer~~]]

OCA at 08:09, 19 January 2022

2022-01-19T08:09:13Z

← Older revision		Revision as of 08:09, 19 January 2022
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	<StructureSection load='2jer' size='340' side='right'caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2jer' size='340' side='right'caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2JER FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JER FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</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=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j2t\|2j2t]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [~~http~~://pdbe.org/2jer PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2jer PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer 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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [https://pdbe.org/2jer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [https://www.ebi.ac.uk/pdbsum/2jer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:49, 15 April 2020

2020-04-15T07:49:28Z

← Older revision		Revision as of 07:49, 15 April 2020
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	==Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.==		==Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.==
	<StructureSection load='2jer' size='340' side='right' caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2jer' size='340' side='right'caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2JER FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2JER FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</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=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://pdbe.org/2jer PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://pdbe.org/2jer PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]		[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
			[[Category: Large Structures]]
	[[Category: Llacer, J L]]		[[Category: Llacer, J L]]
	[[Category: Rubio, V]]		[[Category: Rubio, V]]

OCA at 07:17, 11 July 2018

2018-07-11T07:17:44Z

← Older revision		Revision as of 07:17, 11 July 2018
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	==~~AGMATINE DEIMINASE OF ENTEROCOCCUS FAECALIS CATALYZING ITS REACTION~~.==
			==Agmatine deiminase of Enterococcus faecalis catalyzing its reaction.==
	<StructureSection load='2jer' size='340' side='right' caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2jer' size='340' side='right' caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://pdbe.org/2jer PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer 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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://pdbe.org/2jer PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jer ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/je/2jer_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/je/2jer_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>

OCA at 20:55, 8 February 2016

2016-02-08T20:55:46Z

← Older revision		Revision as of 20:55, 8 February 2016
Line 16:		Line 16:
	<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=2jer ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:18, 10 September 2015

2015-09-10T15:18:38Z

← Older revision		Revision as of 15:18, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2jer' size='340' side='right' caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2jer' size='340' side='right' caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterococcus_faecalis Enterococcus faecalis~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JER FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JER FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</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=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer 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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://pdbe.org/2jer PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2jer" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	~~[[Category: Enterococcus faecalis]]~~
	[[Category: Llacer, J L]]		[[Category: Llacer, J L]]
	[[Category: Rubio, V]]		[[Category: Rubio, V]]

OCA at 17:08, 19 January 2015

2015-01-19T17:08:46Z

← Older revision		Revision as of 17:08, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JER FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JER FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</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=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer 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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer 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 32:		Line 32:
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Enterococcus faecalis]]		[[Category: Enterococcus faecalis]]
	[[Category: Llacer, J L.]]		[[Category: Llacer, J L]]
	[[Category: Rubio, V.]]		[[Category: Rubio, V]]
	[[Category: Tavarez, S.]]		[[Category: Tavarez, S]]
	[[Category: 5- fold pseudosymmetric structure]]		[[Category: 5- fold pseudosymmetric structure]]
	[[Category: Agdi]]		[[Category: Agdi]]
	[[Category: Agmatine degradation pathway]]		[[Category: Agmatine degradation pathway]]
	~~[[Category: Agmatine deiminase]]~~
	[[Category: Agmatine iminohydrolase]]		[[Category: Agmatine iminohydrolase]]
	[[Category: Covalent amidino adduct]]		[[Category: Covalent amidino adduct]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Tetramer]]		[[Category: Tetramer]]

OCA at 10:15, 30 September 2014

2014-09-30T10:15:13Z

← Older revision		Revision as of 10:15, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2jer~~.~~png~~\|~~left~~\|~~200px~~]]		==AGMATINE DEIMINASE OF ENTEROCOCCUS FAECALIS CATALYZING ITS REACTION.==
			<StructureSection load='2jer' size='340' side='right' caption='[[2jer]], [[Resolution\|resolution]] 1.65Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JER FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGT:S-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE'>AGT</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2j2t\|2j2t]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2jer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jer OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jer RCSB], [http://www.ebi.ac.uk/pdbsum/2jer 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/je/2jer_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 ==
			Enterococcus faecalis makes ATP from agmatine in three steps catalyzed by agmatine deiminase (AgDI), putrescine transcarbamylase (PTC), and carbamate kinase (CK). An antiporter exchanges putrescine for agmatine. We have cloned the E. faecalis ef0732 and ef0734 genes of the reported gene cluster for agmatine catabolism, overexpressed them in Escherichia coli, purified the products, characterized them functionally as PTC and AgDI, and crystallized and X-ray diffracted them. The 1.65-Angstroms-resolution structure of AgDI forming a covalent adduct with an agmatine-derived amidine reactional intermediate is described. We provide definitive identification of the gene cluster for agmatine catabolism and confirm that ornithine is a genuine but poor PTC substrate, suggesting that PTC (found here to be trimeric) evolved from ornithine transcarbamylase. N-(Phosphonoacetyl)-putrescine was prepared and shown to strongly (K(i) = 10 nM) and selectively inhibit PTC and to improve PTC crystallization. We find that E. faecalis AgDI, which is committed to ATP generation, closely resembles the AgDIs involved in making polyamines, suggesting the recruitment of a polyamine-synthesizing AgDI into the AgDI pathway. The arginine deiminase (ADI) pathway of arginine catabolism probably supplied the genes for PTC and CK but not those for the agmatine/putrescine antiporter, and thus the AgDI and ADI pathways are not related by a single "en bloc" duplication event. The AgDI crystal structure reveals a tetramer with a five-blade propeller subunit fold, proves that AgDI closely resembles ADI despite a lack of sequence identity, and explains substrate affinity, selectivity, and Cys357-mediated-covalent catalysis. A three-tongued agmatine-triggered gating opens or blocks access to the active center.

	~~{{STRUCTURE_2jer\| PDB=2jer \| SCENE= }}~~		The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction.,Llacer JL, Polo LM, Tavarez S, Alarcon B, Hilario R, Rubio V J Bacteriol. 2007 Feb;189(4):1254-65. Epub 2006 Oct 6. PMID:17028272<ref>PMID:17028272</ref>

	~~===AGMATINE DEIMINASE OF ENTEROCOCCUS FAECALIS CATALYZING ITS REACTION.===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17028272}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2jer]] is~~ a ~~8 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017028272<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Enterococcus faecalis]]		[[Category: Enterococcus faecalis]]

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

2013-01-07T14:43:14Z

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

← Older revision	Revision as of 14:43, 7 January 2013
(No difference)

OCA at 14:43, 7 January 2013

2013-01-07T14:43:13Z

← Older revision		Revision as of 14:43, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2jer.png\|left\|200px]]		[[Image:2jer.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2jer", 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_2jer\| PDB=2jer \| SCENE= }}		{{STRUCTURE_2jer\| PDB=2jer \| SCENE= }}

	===AGMATINE DEIMINASE OF ENTEROCOCCUS FAECALIS CATALYZING ITS REACTION.===		===AGMATINE DEIMINASE OF ENTEROCOCCUS FAECALIS CATALYZING ITS REACTION.===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17028272}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17028272 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17028272}}		{{ABSTRACT_PUBMED_17028272}}

	==About this Structure==		==About this Structure==
	~~2JER~~ is a 8 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA].		[[2jer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j2t 2j2t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JER OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17028272~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017028272</ref><references group="xtra"/>
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Enterococcus faecalis]]		[[Category: Enterococcus faecalis]]
Line 37:		Line 25:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Tetramer]]		[[Category: Tetramer]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 18:23:23 2009''~~