4i5q - Revision history

OCA at 08:43, 9 November 2022

2022-11-09T08:43:01Z

←Older revision		Revision as of 08:43, 9 November 2022
Line 1:		Line 1:

	==Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium==		==Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium==
-	<StructureSection load='4i5q' size='340' side='right' caption='[[4i5q]], [[Resolution\|resolution]] 1.96Å' scene=''>	+	<StructureSection load='4i5q' size='340' side='right'caption='[[4i5q]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i5q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salty Salty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i5q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I5Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbC, STM3043 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])~~</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=4i5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5q OCA], [https://pdbe.org/4i5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i5q RCSB], [https://www.ebi.ac.uk/pdbsum/4i5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5q ProSAT]</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=4i5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5q OCA], [~~http~~://pdbe.org/4i5q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i5q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i5q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5q ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DSBC_SALTY DSBC_SALTY]] Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbC is reoxidized by a yet uncharacterized protein. Also acts as a disulfide isomerase.	+	[https://www.uniprot.org/uniprot/DSBC_SALTY DSBC_SALTY] Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbC is reoxidized by a yet uncharacterized protein. Also acts as a disulfide isomerase.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4i5q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4i5q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thiol:disulfide interchange protein 3D structures\|Thiol:disulfide interchange protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Salty~~]]	+	[[Category: Large Structures]]
-	[[Category: Ha~~, N C~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	[[Category: Kim~~, J S~~]]	+	[[Category: Ha NC]]
-	[[Category: Lee, K]]	+	[[Category: Kim JS]]
-	[[Category: Li, J]]	+	[[Category: Lee K]]
-	[[Category: Yeom~~, J H~~]]	+	[[Category: Li J]]
-	[[Category: Yoon~~, B Y]]~~	+	[[Category: Yeom JH]]
-	~~[[Category: Cxxc motif]]~~	+	[[Category: Yoon BY]]
-	~~[[Category: Disuflide isomerase]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Periplasmic~~]]	+

OCA at 08:50, 15 November 2017

2017-11-15T08:50:34Z

←Older revision		Revision as of 08:50, 15 November 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4i5q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4i5q" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thiol:disulfide interchange protein\|Thiol:disulfide interchange protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:20, 11 August 2016

2016-08-11T12:20:35Z

←Older revision		Revision as of 12:20, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium==		==Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium==
	<StructureSection load='4i5q' size='340' side='right' caption='[[4i5q]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='4i5q' size='340' side='right' caption='[[4i5q]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I5Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbC, STM3043 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 ~~Salmonella enterica subsp. enterica serovar Typhimurium str. LT2~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbC, STM3043 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=4i5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i5q RCSB], [http://www.ebi.ac.uk/pdbsum/4i5q 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=4i5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5q OCA], [http://pdbe.org/4i5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i5q RCSB], [http://www.ebi.ac.uk/pdbsum/4i5q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DSBC_SALTY DSBC_SALTY]] Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbC is reoxidized by a yet uncharacterized protein. Also acts as a disulfide isomerase.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 18:
	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 4i5q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thiol:disulfide interchange protein\|Thiol:disulfide interchange protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Salmonella enterica subsp. enterica serovar typhimurium str. lt2~~]]	+	[[Category: Salty]]
	[[Category: Ha, N C]]		[[Category: Ha, N C]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]

OCA at 14:30, 4 January 2015

2015-01-04T14:30:59Z

←Older revision		Revision as of 14:30, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4i5q\| PDB=4i5q \| SCENE= }}~~	+	==Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium==
-	===Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium===	+	<StructureSection load='4i5q' size='340' side='right' caption='[[4i5q]], [[Resolution\|resolution]] 1.96Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23726983}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4i5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I5Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbC, STM3043 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2])</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=4i5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i5q RCSB], [http://www.ebi.ac.uk/pdbsum/4i5q PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The disulfide-bond isomerase DsbC plays a crucial role in the folding of bacterial proteins in the periplasmic space. DsbC has a V-shaped dimeric structure with two domains, and Cys98 in the C-terminal domain attacks inappropriate disulfide bonds in substrate proteins due to its high nucleophilic activity. In this article, we present the crystal structure of DsbC from Salmonella enterica serovar Typhimurium. We evaluated the conserved residues Asp95 and Arg125, which are located close to Cys98. The mutation of Asp95 or Arg125 abolished the disulfide isomerase activity of DsbC in an in vitro assay using a protein substrate, and the R125A mutation significantly reduced the chaperone activity for the substrate RNase I in vivo. Furthermore, a comparative analysis suggested that the conformation of Arg125 varies depending on the packing or protein-protein interactions. Based on these findings, we suggest that Asp95 and Arg125 modulate the pKa of Cys98 during catalysis.

-	~~==About this Structure==~~	+	Crystal structure of the periplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium and the mechanistic implications.,Jiao L, Kim JS, Song WS, Yoon BY, Lee K, Ha NC J Struct Biol. 2013 Jul;183(1):1-10. doi: 10.1016/j.jsb.2013.05.013. Epub 2013, May 29. PMID:23726983<ref>PMID:23726983</ref>
-	~~[[4i5q]] is a 2 chain~~ structure ~~with sequence~~ from ~~[http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Salmonella_enterica_subsp~~.~~_enterica_serovar_typhimurium_str~~.~~_lt2 Salmonella enterica subsp~~. ~~enterica serovar typhimurium str~~. ~~lt2]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4I5Q OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023726983</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]
-	[[Category: Ha, N C.]]	+	[[Category: Ha, N C]]
-	[[Category: Kim, J S.]]	+	[[Category: Kim, J S]]
-	[[Category: Lee, K.]]	+	[[Category: Lee, K]]
-	[[Category: Li, J.]]	+	[[Category: Li, J]]
-	[[Category: Yeom, J H.]]	+	[[Category: Yeom, J H]]
-	[[Category: Yoon, B Y.]]	+	[[Category: Yoon, B Y]]
	[[Category: Cxxc motif]]		[[Category: Cxxc motif]]
	[[Category: Disuflide isomerase]]		[[Category: Disuflide isomerase]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Periplasmic]]		[[Category: Periplasmic]]

OCA at 08:00, 16 October 2013

2013-10-16T08:00:36Z

←Older revision		Revision as of 08:00, 16 October 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4i5q\| PDB=4i5q \| SCENE= }}
		+	===Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium===
		+	{{ABSTRACT_PUBMED_23726983}}

-	~~The entry~~ 4i5q is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4i5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5Q OCA].

-	~~Authors~~: Ha, N.C.~~, Li, J.,~~ Kim, J.S., ~~Yoon, B.Y~~., Yeom, J.H., ~~Lee, K~~.	+	==Reference==
-		+	<ref group="xtra">PMID:023726983</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure and catalytic mechanism for peroplasmic disulfide-bond~~ isomerase ~~DsbC from Salmonella enterica serovar Typhimurium~~	+	[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]
		+	[[Category: Ha, N C.]]
		+	[[Category: Kim, J S.]]
		+	[[Category: Lee, K.]]
		+	[[Category: Li, J.]]
		+	[[Category: Yeom, J H.]]
		+	[[Category: Yoon, B Y.]]
		+	[[Category: Cxxc motif]]
		+	[[Category: Disuflide isomerase]]
		+	[[Category: Isomerase]]
		+	[[Category: Periplasmic]]

OCA at 16:12, 20 March 2013

2013-03-20T16:12:09Z

←Older revision		Revision as of 16:12, 20 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i5q is ON HOLD	+	The entry 4i5q is ON HOLD until Paper Publication

	Authors: Ha, N.C., Li, J., Kim, J.S., Yoon, B.Y., Yeom, J.H., Lee, K.		Authors: Ha, N.C., Li, J., Kim, J.S., Yoon, B.Y., Yeom, J.H., Lee, K.

	Description: Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium		Description: Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium

OCA at 20:48, 12 December 2012

2012-12-12T20:48:12Z

←Older revision		Revision as of 20:48, 12 December 2012
Line 3:		Line 3:
	The entry 4i5q is ON HOLD		The entry 4i5q is ON HOLD

-	Authors: ~~Nam-Chul~~ Ha, Li ~~JIao~~, ~~Jin-SiK~~ Kim, ~~Bo-Young~~ Yoon, ~~Ji-Hyun~~ Yeom, ~~KangseoK~~ Lee	+	Authors: Ha, N.C., Li, J., Kim, J.S., Yoon, B.Y., Yeom, J.H., Lee, K.

	Description: Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium		Description: Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium

OCA: Protected "4i5q" [edit=sysop:move=sysop]

2012-12-05T10:35:21Z

Protected "4i5q" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:35, 5 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i5q is ON HOLD Authors: Nam-Chul Ha, Li JIao, Jin-SiK Kim, Bo-Young Yoon, Ji-Hyun Yeom, KangseoK Lee Description: Crystal structure and catalytic ...

2012-12-05T10:35:20Z

New page: '''Unreleased structure''' The entry 4i5q is ON HOLD Authors: Nam-Chul Ha, Li JIao, Jin-SiK Kim, Bo-Young Yoon, Ji-Hyun Yeom, KangseoK Lee Description: Crystal structure and catalytic ...

New page

'''Unreleased structure'''

The entry 4i5q is ON HOLD

Authors: Nam-Chul Ha, Li JIao, Jin-SiK Kim, Bo-Young Yoon, Ji-Hyun Yeom, KangseoK Lee

Description: Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium