2e2m - Revision history

OCA at 05:10, 17 October 2024

2024-10-17T05:10:53Z

← Older revision		Revision as of 05:10, 17 October 2024
Line 15:		Line 15:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e2m_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e2m_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 08:34, 25 October 2023

2023-10-25T08:34:07Z

← Older revision		Revision as of 08:34, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2e2m' size='340' side='right'caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2e2m' size='340' side='right'caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aerpe Aerpe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E2M FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E2M FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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]] 2.6Å</td></tr>
	~~<tr~~ id~~='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class~~="~~sblockDat~~">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[2e2g\|2e2g]]~~, [[~~2nvl~~\|~~2nvl~~]]~~</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15]~~ </~~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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [https://pdbe.org/2e2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [https://www.ebi.ac.uk/pdbsum/2e2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e2m 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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [https://pdbe.org/2e2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [https://www.ebi.ac.uk/pdbsum/2e2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e2m ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/TDXH_AERPE TDXH_AERPE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Aerpe~~]]		[[Category: Aeropyrum pernix K1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Peroxiredoxin]]~~		[[Category: Abe M]]
	[[Category: Abe, M]]		[[Category: Goto T]]
	[[Category: Goto, T]]		[[Category: Hagihara Y]]
	[[Category: Hagihara, Y]]		[[Category: Inoue T]]
	[[Category: Inoue, T]]		[[Category: Matsumura H]]
	[[Category: Matsumura, H]]		[[Category: Nakamura T]]
	[[Category: Nakamura, T]]		[[Category: Yamaguchi T]]
	[[Category: Yamaguchi, T]]		[[Category: Yamamoto T]]
	[[Category: Yamamoto, T]]
	~~[[Category: Cysteine sulfenic acid]]~~
	~~[[Category: Cysteine sulfinic acid]]~~
	~~[[Category: Cysteine sulfonic acid]]~~
	~~[[Category: Hypervalent sulfur compound]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Peroxidatic cysteine~~]]

OCA at 06:53, 10 November 2021

2021-11-10T06:53:37Z

← Older revision		Revision as of 06:53, 10 November 2021
Line 3:		Line 3:
	<StructureSection load='2e2m' size='340' side='right'caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2e2m' size='340' side='right'caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2E2M FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E2M FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e2g\|2e2g]], [[2nvl\|2nvl]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [~~http~~://pdbe.org/2e2m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2e2m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2e2m 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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [https://pdbe.org/2e2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [https://www.ebi.ac.uk/pdbsum/2e2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e2m ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:26, 11 March 2020

2020-03-11T08:26:05Z

← Older revision		Revision as of 08:26, 11 March 2020
Line 1:		Line 1:

	==Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)==		==Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)==
	<StructureSection load='2e2m' size='340' side='right' caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2e2m' size='340' side='right'caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E2M FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E2M FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Aerpe]]		[[Category: Aerpe]]
			[[Category: Large Structures]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]
	[[Category: Abe, M]]		[[Category: Abe, M]]

OCA at 06:49, 6 June 2018

2018-06-06T06:49:28Z

← Older revision		Revision as of 06:49, 6 June 2018
Line 1:		Line 1:

	==Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)==		==Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)==
	<StructureSection load='2e2m' size='340' side='right' caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2e2m' size='340' side='right' caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [http://pdbe.org/2e2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [http://www.ebi.ac.uk/pdbsum/2e2m 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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [http://pdbe.org/2e2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [http://www.ebi.ac.uk/pdbsum/2e2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e2m ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e2m_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e2m_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=2e2m ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:04, 11 September 2015

2015-09-11T23:04:15Z

← Older revision		Revision as of 23:04, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2e2m' size='340' side='right' caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2e2m' size='340' side='right' caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aeropyrum_pernix Aeropyrum pernix~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E2M FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E2M FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [http://www.ebi.ac.uk/pdbsum/2e2m 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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [http://pdbe.org/2e2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [http://www.ebi.ac.uk/pdbsum/2e2m PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 2e2m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Aeropyrum pernix~~]]		[[Category: Aerpe]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]
	[[Category: Abe, M]]		[[Category: Abe, M]]

OCA at 17:56, 15 January 2015

2015-01-15T17:56:58Z

← Older revision		Revision as of 17:56, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E2M FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E2M FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</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=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [http://www.ebi.ac.uk/pdbsum/2e2m 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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [http://www.ebi.ac.uk/pdbsum/2e2m 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: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]
	[[Category: Abe, M.]]		[[Category: Abe, M]]
	[[Category: Goto, T.]]		[[Category: Goto, T]]
	[[Category: Hagihara, Y.]]		[[Category: Hagihara, Y]]
	[[Category: Inoue, T.]]		[[Category: Inoue, T]]
	[[Category: Matsumura, H.]]		[[Category: Matsumura, H]]
	[[Category: Nakamura, T.]]		[[Category: Nakamura, T]]
	[[Category: Yamaguchi, T.]]		[[Category: Yamaguchi, T]]
	[[Category: Yamamoto, T.]]		[[Category: Yamamoto, T]]
	[[Category: Cysteine sulfenic acid]]		[[Category: Cysteine sulfenic acid]]
	[[Category: Cysteine sulfinic acid]]		[[Category: Cysteine sulfinic acid]]

OCA at 02:38, 30 September 2014

2014-09-30T02:38:52Z

← Older revision		Revision as of 02:38, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2e2m~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)==
			<StructureSection load='2e2m' size='340' side='right' caption='[[2e2m]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E2M FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2e2g\|2e2g]], [[2nvl\|2nvl]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=2e2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e2m RCSB], [http://www.ebi.ac.uk/pdbsum/2e2m 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/e2/2e2m_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 ==
			The oxidation of thiol groups in proteins is a common event in biochemical processes involving disulfide bond formation and in response to an increased level of reactive oxygen species. It has been widely accepted that the oxidation of a cysteine side chain is initiated by the formation of cysteine sulfenic acid (Cys-SOH). Here, we demonstrate a mechanism of thiol oxidation through a hypervalent sulfur intermediate by presenting crystallographic evidence from an archaeal peroxiredoxin (Prx), the thioredoxin peroxidase from Aeropyrum pernix K1 (ApTPx). The reaction of Prx, which is the reduction of a peroxide, depends on the redox active cysteine side chains. Oxidation by hydrogen peroxide converted the active site peroxidatic Cys-50 of ApTPx to a cysteine sulfenic acid derivative, followed by further oxidation to cysteine sulfinic and sulfonic acids. The crystal structure of the cysteine sulfenic acid derivative was refined to 1.77 A resolution with R(cryst) and R(free) values of 18.8% and 22.0%, respectively. The refined structure, together with quantum chemical calculations, revealed that the sulfenic acid derivative is a type of sulfurane, a hypervalent sulfur compound, and that the S(gamma) atom is covalently linked to the N(delta1) atom of the neighboring His-42. The reaction mechanism is revealed by the hydrogen bond network around the peroxidatic cysteine and the motion of the flexible loop covering the active site and by quantum chemical calculations. This study provides evidence that a hypervalent sulfur compound occupies an important position in biochemical processes.

	~~{{STRUCTURE_2e2m\| PDB=2e2m \| SCENE= }}~~		Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate.,Nakamura T, Yamamoto T, Abe M, Matsumura H, Hagihara Y, Goto T, Yamaguchi T, Inoue T Proc Natl Acad Sci U S A. 2008 Apr 29;105(17):6238-42. Epub 2008 Apr 24. PMID:18436649<ref>PMID:18436649</ref>

	~~===Crystal structure of archaeal peroxiredoxin~~, ~~thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18436649}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2e2m]] is~~ a ~~10 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aeropyrum_pernix Aeropyrum pernix]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018436649<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]

OCA: Protected "2e2m" [edit=sysop:move=sysop]

2013-01-06T11:51:37Z

Protected "2e2m" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:51, 6 January 2013
(No difference)

OCA at 11:51, 6 January 2013

2013-01-06T11:51:35Z

← Older revision		Revision as of 11:51, 6 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2e2m.png\|left\|200px]]		[[Image:2e2m.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2e2m", 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_2e2m\| PDB=2e2m \| SCENE= }}		{{STRUCTURE_2e2m\| PDB=2e2m \| SCENE= }}

	===Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)===		===Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18436649}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18436649 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18436649}}		{{ABSTRACT_PUBMED_18436649}}

	==About this Structure==		==About this Structure==
	~~2E2M~~ is a 10 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA].		[[2e2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2M OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18436649~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018436649</ref><references group="xtra"/>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]
Line 40:		Line 28:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Peroxidatic cysteine]]		[[Category: Peroxidatic cysteine]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:29:44 2009''~~