2fwe - Revision history

OCA at 07:53, 23 October 2024

2024-10-23T07:53:59Z

← Older revision		Revision as of 07:53, 23 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fw/2fwe_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fw/2fwe_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 08:45, 25 October 2023

2023-10-25T08:45:59Z

← Older revision		Revision as of 08:45, 25 October 2023
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	<StructureSection load='2fwe' size='340' side='right'caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2fwe' size='340' side='right'caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FWE FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~, ~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 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;'>[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DSBD, DIPZ, CYCZ, CUTA2, B4136 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~<~~/td~~></tr>
	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8]~~ </~~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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [https://pdbe.org/2fwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [https://www.ebi.ac.uk/pdbsum/2fwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fwe 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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [https://pdbe.org/2fwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [https://www.ebi.ac.uk/pdbsum/2fwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fwe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DSBD_ECOLI DSBD_ECOLI]] Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]		[https://www.uniprot.org/uniprot/DSBD_ECOLI DSBD_ECOLI] Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]
	== 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: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Protein-disulfide reductase]]~~		[[Category: Boeckmann RA]]
	[[Category: Boeckmann~~, R A~~]]		[[Category: Capitani G]]
	[[Category: Capitani, G]]		[[Category: Glockshuber R]]
	[[Category: Glockshuber, R]]		[[Category: Grauschopf U]]
	[[Category: Grauschopf, U]]		[[Category: Gruetter MG]]
	[[Category: Gruetter~~, M G~~]]		[[Category: Rozhkova A]]
	[[Category: Rozhkova, A]]		[[Category: Stirnimann CU]]
	[[Category: Stirnimann~~, C U]]~~
	~~[[Category: C-terminal domain]]~~
	~~[[Category: Dsbd]]~~
	~~[[Category: Oxidized form]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Thioredoxin-like~~]]

OCA at 15:34, 3 March 2021

2021-03-03T15:34:44Z

← Older revision		Revision as of 15:34, 3 March 2021
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	==crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)==		==crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)==
	<StructureSection load='2fwe' size='340' side='right' caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2fwe' size='340' side='right'caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FWE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [~~http~~://pdbe.org/2fwe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fwe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fwe 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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [https://pdbe.org/2fwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [https://www.ebi.ac.uk/pdbsum/2fwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fwe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DSBD_ECOLI DSBD_ECOLI]] Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]		[[https://www.uniprot.org/uniprot/DSBD_ECOLI DSBD_ECOLI]] Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Thiol:disulfide interchange protein\|Thiol:disulfide interchange protein]]		*[[Thiol:disulfide interchange protein 3D structures\|Thiol:disulfide interchange protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: Protein-disulfide reductase]]		[[Category: Protein-disulfide reductase]]
	[[Category: Boeckmann, R A]]		[[Category: Boeckmann, R A]]

OCA at 07:07, 20 June 2018

2018-06-20T07:07:57Z

← Older revision		Revision as of 07:07, 20 June 2018
Line 1:		Line 1:

	==crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)==		==crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)==
	<StructureSection load='2fwe' size='340' side='right' caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2fwe' size='340' side='right' caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://pdbe.org/2fwe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe 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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://pdbe.org/2fwe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fwe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/fw/2fwe_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fw/2fwe_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 11:11, 7 February 2016

2016-02-07T11:11:30Z

← Older revision		Revision as of 11:11, 7 February 2016
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	<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=2fwe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:56, 10 September 2015

2015-09-10T00:56:21Z

← Older revision		Revision as of 00:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2fwe' size='340' side='right' caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2fwe' size='340' side='right' caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FWE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe 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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://pdbe.org/2fwe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 2fwe" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Thiol:disulfide interchange protein\|Thiol:disulfide interchange protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Protein-disulfide reductase]]		[[Category: Protein-disulfide reductase]]
	[[Category: Boeckmann, R A]]		[[Category: Boeckmann, R A]]

OCA at 14:38, 24 December 2014

2014-12-24T14:38:34Z

← Older revision		Revision as of 14:38, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FWE FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe 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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DSBD_ECOLI DSBD_ECOLI]] Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Protein-disulfide reductase]]		[[Category: Protein-disulfide reductase]]
	[[Category: Boeckmann, R A.]]		[[Category: Boeckmann, R A]]
	[[Category: Capitani, G.]]		[[Category: Capitani, G]]
	[[Category: Glockshuber, R.]]		[[Category: Glockshuber, R]]
	[[Category: Grauschopf, U.]]		[[Category: Grauschopf, U]]
	[[Category: Gruetter, M G.]]		[[Category: Gruetter, M G]]
	[[Category: Rozhkova, A.]]		[[Category: Rozhkova, A]]
	[[Category: Stirnimann, C U.]]		[[Category: Stirnimann, C U]]
	[[Category: C-terminal domain]]		[[Category: C-terminal domain]]
	[[Category: Dsbd]]		[[Category: Dsbd]]

OCA at 08:03, 30 September 2014

2014-09-30T08:03:16Z

← Older revision		Revision as of 08:03, 30 September 2014
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	[[Image:~~2fwe~~.~~png~~\|~~left~~\|~~200px~~]]		==crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)==
			<StructureSection load='2fwe' size='340' side='right' caption='[[2fwe]], [[Resolution\|resolution]] 1.65Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FWE FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fwf\|2fwf]], [[2fwg\|2fwg]], [[2fwh\|2fwh]], [[1vrs\|1vrs]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-disulfide_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe 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/fw/2fwe_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 ==
			Escherichia coli DsbD transports electrons from cytoplasmic thioredoxin to periplasmic target proteins. DsbD is composed of an N-terminal (nDsbD) and a C-terminal (cDsbD) periplasmic domain, connected by a central transmembrane domain. Each domain possesses two cysteine residues essential for electron transport. The transport proceeds via disulfide exchange reactions from cytoplasmic thioredoxin to the central transmembrane domain and via cDsbD to nDsbD, which then reduces the periplasmic target proteins. We determined four high-resolution structures of cDsbD: oxidized (1.65 A resolution), chemically reduced (1.3 A), photo-reduced (1.1 A) and chemically reduced at pH increased from 4.6 to 7. The latter structure was refined at 0.99 A resolution, the highest achieved so far for a thioredoxin superfamily member. The data reveal unprecedented structural details of cDsbD, demonstrating that the domain is very rigid and undergoes hardly any conformational change upon disulfide reduction or interaction with nDsbD. In full agreement with the crystallographic results, guanidinium chloride-induced unfolding and refolding experiments indicate that oxidized and reduced cDsbD are equally stable. We confirmed the structural rigidity of cDsbD by molecular dynamics simulations. A remarkable feature of cDsbD is the pKa of 9.3 for the active site Cys461: this value, determined using two different experimental methods, surprisingly was around 2.5 units higher than expected on the basis of the redox potential. Additionally, taking advantage of the very high quality of the cDsbD structures, we carried out pKa calculations, which gave results in agreement with the experimental findings. In conclusion, our wide-scope analysis of cDsbD, encompassing atomic-resolution crystallography, computational chemistry and biophysical measurements, highlighted two so far unrecognized key aspects of this domain: its unusual redox properties and extreme rigidity. Both are likely to be correlated to the role of cDsbD as a covalently linked electron shuttle between the membrane domain and the N-terminal periplasmic domain of DsbD.

	~~{{STRUCTURE_2fwe\| PDB=2fwe \| SCENE= }}~~		High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study.,Stirnimann CU, Rozhkova A, Grauschopf U, Bockmann RA, Glockshuber R, Capitani G, Grutter MG J Mol Biol. 2006 May 5;358(3):829-45. Epub 2006 Feb 28. PMID:16545842<ref>PMID:16545842</ref>

	~~===crystal structure of the C-terminal domain~~ of the ~~electron transfer catalyst DsbD (oxidized form)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16545842}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2fwe]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016545842<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Protein-disulfide reductase]]		[[Category: Protein-disulfide reductase]]

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

2013-01-07T13:07:39Z

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

← Older revision	Revision as of 13:07, 7 January 2013
(No difference)

OCA at 13:07, 7 January 2013

2013-01-07T13:07:36Z

← Older revision		Revision as of 13:07, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2fwe.png\|left\|200px]]		[[Image:2fwe.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2fwe", 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_2fwe\| PDB=2fwe \| SCENE= }}		{{STRUCTURE_2fwe\| PDB=2fwe \| SCENE= }}

	===crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)===		===crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16545842}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16545842 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16545842}}		{{ABSTRACT_PUBMED_16545842}}

	==About this Structure==		==About this Structure==
	~~2FWE~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA].		[[2fwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16545842~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016545842</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Protein-disulfide reductase]]		[[Category: Protein-disulfide reductase]]
Line 36:		Line 24:
	[[Category: Dsbd]]		[[Category: Dsbd]]
	[[Category: Oxidized form]]		[[Category: Oxidized form]]
			[[Category: Oxidoreductase]]
	[[Category: Thioredoxin-like]]		[[Category: Thioredoxin-like]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:24:44 2009''~~