6dps - Revision history

OCA at 05:09, 21 November 2024

2024-11-21T05:09:56Z

← Older revision		Revision as of 05:09, 21 November 2024
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	==Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the oxidised form==		==Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the oxidised form==
	<StructureSection load='6dps' size='340' side='right' caption='[[6dps]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='6dps' size='340' side='right'caption='[[6dps]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dps]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Neiml Neiml~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dps]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_alpha14 Neisseria meningitidis alpha14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DPS FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.556Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">dsbD, NMO_1340 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5~~&~~id=662598 NEIML])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6dps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dps OCA], [https://pdbe.org/6dps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dps RCSB], [https://www.ebi.ac.uk/pdbsum/6dps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dps 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=6dps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dps OCA], [~~http~~://pdbe.org/6dps PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dps RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dps PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dps ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/C6S7X6_NEIML C6S7X6_NEIML]] 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. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]		[https://www.uniprot.org/uniprot/C6S7X6_NEIML C6S7X6_NEIML] 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. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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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/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Neiml~~]]		[[Category: Large Structures]]
	[[Category: ~~Protein-disulfide reductase~~]]		[[Category: Neisseria meningitidis alpha14]]
	[[Category: Heras, B]]		[[Category: Heras B]]
	[[Category: Paxman~~, J J~~]]		[[Category: Paxman JJ]]
	[[Category: Smith~~, R P]]~~		[[Category: Smith RP]]
	~~[[Category: Disulphide reductase]]~~
	~~[[Category: Dsb protein]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 12:43, 7 November 2018

2018-11-07T12:43:55Z

← Older revision		Revision as of 12:43, 7 November 2018
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	</div>		</div>
	<div class="pdbe-citations 6dps" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dps" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Thiol:disulfide interchange protein\|Thiol:disulfide interchange protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:19, 19 September 2018

2018-09-19T20:19:36Z

← Older revision		Revision as of 20:19, 19 September 2018
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	<StructureSection load='6dps' size='340' side='right' caption='[[6dps]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='6dps' size='340' side='right' caption='[[6dps]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dps]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DPS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dps]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Neiml Neiml]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DPS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsbD, NMO_1340 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=662598 NEIML])</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=6dps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dps OCA], [http://pdbe.org/6dps PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dps RCSB], [http://www.ebi.ac.uk/pdbsum/6dps PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dps 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=6dps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dps OCA], [http://pdbe.org/6dps PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dps RCSB], [http://www.ebi.ac.uk/pdbsum/6dps PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dps ProSAT]</span></td></tr>
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	The ~~membrane protein DsbD~~ is ~~a reductase~~ that ~~acts as an electron hub, translocating reducing equivalents from cytoplasmic thioredoxin~~ to a ~~number~~ of ~~periplasmic substrates involved in oxidative protein folding~~, ~~cytochrome c maturation~~ and ~~oxidative stress defence~~. DsbD is a ~~multi-domain~~ protein ~~consisting~~ of ~~a transmembrane domain (t-DsbD) flanked by~~ two periplasmic domains (n-DsbD and c-DsbD~~). Previous studies have shown that~~ DsbD ~~is required for the survival of the obligate human pathogen Neisseria meningitidis~~. ~~To help understand~~ the ~~structural and functional aspects of N. meningitidis DsbD,~~ the two periplasmic domains ~~which are required for~~ electron transfer ~~are being studied. Here~~, ~~the expression, purification and biophysical properties of~~ n-~~NmDsbD~~ and ~~c-NmDsbD are described~~. ~~The crystallization and crystallographic analysis~~ of n-~~NmDsbD~~ and c-~~NmDsbD are also described~~ in both redox states~~, which differ only in~~ the ~~presence or absence of a disulfide bond but which crystallized in completely different conditions. Crystals of~~ n-~~NmDsbDOx~~, ~~n-NmDsbDRed~~, ~~c-NmDsbDOx~~ and c-~~NmDsbDRed diffracted to 2~~.~~3, 1.6, 2.3 and 1.7 A resolution and belonged~~ to ~~space groups P213, P321, P41 and P1211, respectively~~.		The worldwide incidence of neisserial infections, particularly gonococcal infections, is increasingly associated with antibiotic resistant strains. In particular, extensively drug-resistant Neisseria gonorrhoeae strains that are resistant to third-generation cephalosporins are a major public health concern. There is a pressing clinical need to identify new targets for the development of antibiotics effective against neisserial-specific processes. In this study, we report that the bacterial disulfide reductase DsbD is highly prevalent and conserved amongst Neisseria spp. and that this enzyme is essential for survival of N. gonorrhoeae DsbD is a membrane bound protein that consists of two periplasmic domains, n-DsbD and c-DsbD, which flank the transmembrane domain t-DsbD. In the current work we show that the two functionally essential periplasmic domains of Neisseria DsbD catalyze electron transfer reactions through unidirectional inter-domain interactions, from reduced c-DsbD to oxidized n-DsbD, and that this process is not dictated by their redox potentials. Structural characterization of Neisseria n- and c-DsbD domains in both redox states provides evidence that steric hindrance reduces interactions between the two periplasmic domains when n-DsbD is reduced, thereby preventing a futile redox cycle. Finally, we propose a conserved mechanism of electron transfer for DsbD and define the residues involved in domain-domain recognition. Inhibitors of the interaction of the two DsbD domains have the potential to be developed as anti-neisserial agents.

	~~Production, biophysical characterization~~ and ~~initial crystallization studies of~~ the ~~N- and C-terminal domains~~ of DsbD, an essential enzyme ~~in Neisseria meningitidis~~.,Smith RP, ~~Whitten AE~~, Paxman JJ, Kahler CM, Scanlon MJ, Heras B ~~Acta Crystallogr F Struct~~ Biol ~~Commun~~. 2018 ~~Jan 1;74(Pt 1)~~:~~31-38~~. doi:, 10.~~1107~~/~~S2053230X17017800~~. ~~Epub 2018 Jan 1~~. PMID:~~29372905~~<ref>PMID:~~29372905~~</ref>		Structural and biochemical insights into the disulfide reductase mechanism of DsbD, an essential enzyme for neisserial pathogens.,Smith RP, Mohanty B, Mowlaboccus S, Paxman JJ, Williams ML, Headey SJ, Wang G, Subedi P, Doak BC, Kahler CM, Scanlon MJ, Heras B J Biol Chem. 2018 Sep 4. pii: RA118.004847. doi: 10.1074/jbc.RA118.004847. PMID:30181210<ref>PMID:30181210</ref>

	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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Neiml]]
	[[Category: Protein-disulfide reductase]]		[[Category: Protein-disulfide reductase]]
	[[Category: Heras, B]]		[[Category: Heras, B]]

OCA at 07:36, 12 September 2018

2018-09-12T07:36:35Z

@@ Line 1: / Line 1: @@
-The entry 6dps is ON HOLD  until Paper Publication
+==Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the oxidised form==
-Authors: Heras, B., Smith, R.P., Paxman, J.J.
+Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.,Smith RP, Whitten AE, Paxman JJ, Kahler CM, Scanlon MJ, Heras B Acta Crystallogr F Struct Biol Commun. 2018 Jan 1;74(Pt 1):31-38. doi:, 10.1107/S2053230X17017800. Epub 2018 Jan 1. PMID:29372905<ref>PMID:29372905</ref>
-Description: Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the oxidised form
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
 [[Category: Heras, B]]
-[[Category: Smith, R.P]]
+[[Category: Paxman, J J]]
-[[Category: Paxman, J.J]]
+[[Category: Smith, R P]]

OCA at 05:39, 4 July 2018

2018-07-04T05:39:37Z

← Older revision		Revision as of 05:39, 4 July 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6dps is ON HOLD		The entry 6dps is ON HOLD until Paper Publication

	Authors: Heras, B., Smith, R.P., Paxman, J.J.		Authors: Heras, B., Smith, R.P., Paxman, J.J.

OCA: Protected "6dps" [edit=sysop:move=sysop]

2018-06-20T04:06:24Z

Protected "6dps" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:06, 20 June 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6dps is ON HOLD Authors: Heras, B., Smith, R.P., Paxman, J.J. Description: Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in th...

2018-06-20T04:06:23Z

New page: '''Unreleased structure''' The entry 6dps is ON HOLD Authors: Heras, B., Smith, R.P., Paxman, J.J. Description: Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in th...

New page

'''Unreleased structure'''

The entry 6dps is ON HOLD

Authors: Heras, B., Smith, R.P., Paxman, J.J.

Description: Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the oxidised form
[[Category: Unreleased Structures]]
[[Category: Heras, B]]
[[Category: Smith, R.P]]
[[Category: Paxman, J.J]]