6g81 - Revision history

OCA at 10:47, 14 June 2023

OCA — Wed, 14 Jun 2023 10:47:21 GMT

←Older revision		Revision as of 10:47, 14 June 2023
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	==Solution structure of the Ni metallochaperone HypA from Helicobacter pylori==		==Solution structure of the Ni metallochaperone HypA from Helicobacter pylori==
-	<StructureSection load='6g81' size='340' side='right'caption='[[6g81~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='6g81' size='340' side='right'caption='[[6g81]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6g81]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori_j99 Campylobacter~~ pylori ~~j99~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G81 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6G81 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6g81]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_J99 Helicobacter pylori J99]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6G81 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" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hypA, jhp_0803 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85963 Campylobacter pylori J99])</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=6g81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g81 OCA], [https://pdbe.org/6g81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6g81 RCSB], [https://www.ebi.ac.uk/pdbsum/6g81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6g81 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=6g81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g81 OCA], [~~http~~://pdbe.org/6g81 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6g81 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6g81 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6g81 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HYPA_HELPJ HYPA_HELPJ]] Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase.[HAMAP-Rule:MF_00213]	+	[https://www.uniprot.org/uniprot/HYPA_HELPJ HYPA_HELPJ] Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase.[HAMAP-Rule:MF_00213]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6g81" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6g81" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures\|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori ~~j99~~]]	+	[[Category: Helicobacter pylori J99]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bardiaux, B]]	+	[[Category: Bardiaux B]]
-	[[Category: Ciurli, S]]	+	[[Category: Ciurli S]]
-	[[Category: Gorka, M]]	+	[[Category: Gorka M]]
-	[[Category: Hu, H]]	+	[[Category: Hu H]]
-	[[Category: Kozminski, W]]	+	[[Category: Kozminski W]]
-	[[Category: Maroney, M]]	+	[[Category: Maroney M]]
-	[[Category: Musiani, F]]	+	[[Category: Musiani F]]
-	[[Category: Piccioli, M]]	+	[[Category: Piccioli M]]
-	[[Category: Spronk~~, C A.E M~~]]	+	[[Category: Spronk CAEM]]
-	[[Category: Zambelli, B]]	+	[[Category: Zambelli B]]
-	[[Category: Zerko, S]]	+	[[Category: Zerko S]]
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Metallochaperone metal-binding nickel hydrogenase~~]]	+

OCA at 13:29, 10 May 2019

OCA — Fri, 10 May 2019 13:29:56 GMT

←Older revision		Revision as of 13:29, 10 May 2019
Line 1:		Line 1:

	==Solution structure of the Ni metallochaperone HypA from Helicobacter pylori==		==Solution structure of the Ni metallochaperone HypA from Helicobacter pylori==
-	<StructureSection load='6g81' size='340' side='right' caption='[[6g81]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='6g81' size='340' side='right'caption='[[6g81]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6g81]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G81 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6g81]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G81 FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Campylobacter pylori j99]]		[[Category: Campylobacter pylori j99]]
		+	[[Category: Large Structures]]
	[[Category: Bardiaux, B]]		[[Category: Bardiaux, B]]
	[[Category: Ciurli, S]]		[[Category: Ciurli, S]]

OCA at 07:05, 5 December 2018

OCA — Wed, 05 Dec 2018 07:05:41 GMT

←Older revision		Revision as of 07:05, 5 December 2018
Line 3:		Line 3:
	<StructureSection load='6g81' size='340' side='right' caption='[[6g81]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='6g81' size='340' side='right' caption='[[6g81]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6g81]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G81 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6g81]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G81 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">hypA, jhp_0803 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85963 Campylobacter pylori J99])</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=6g81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g81 OCA], [http://pdbe.org/6g81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g81 RCSB], [http://www.ebi.ac.uk/pdbsum/6g81 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g81 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=6g81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g81 OCA], [http://pdbe.org/6g81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g81 RCSB], [http://www.ebi.ac.uk/pdbsum/6g81 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g81 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori j99]]
	[[Category: Bardiaux, B]]		[[Category: Bardiaux, B]]
	[[Category: Ciurli, S]]		[[Category: Ciurli, S]]

OCA at 08:12, 10 October 2018

OCA — Wed, 10 Oct 2018 08:12:55 GMT

←Older revision		Revision as of 08:12, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6g81 is ~~ON HOLD until Paper~~ Publication	+	==Solution structure of the Ni metallochaperone HypA from Helicobacter pylori==
		+	<StructureSection load='6g81' size='340' side='right' caption='[[6g81]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6g81]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G81 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>
		+	<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=6g81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g81 OCA], [http://pdbe.org/6g81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g81 RCSB], [http://www.ebi.ac.uk/pdbsum/6g81 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g81 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HYPA_HELPJ HYPA_HELPJ]] Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase.[HAMAP-Rule:MF_00213]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3-7.2 range. The structure of the Ni(II) binding site was probed using (1)H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.

-	~~Authors~~: ~~Spronk~~, ~~C.A.E.M~~., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Hu, H., Maroney, M., Ciurli, S.	+	Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools.,Spronk CAEM, Zerko S, Gorka M, Kozminski W, Bardiaux B, Zambelli B, Musiani F, Piccioli M, Basak P, Blum FC, Johnson RC, Hu H, Merrell DS, Maroney M, Ciurli S J Biol Inorg Chem. 2018 Sep 27. pii: 10.1007/s00775-018-1616-y. doi:, 10.1007/s00775-018-1616-y. PMID:30264175<ref>PMID:30264175</ref>

-	~~Description: Solution structure~~ of the ~~Ni metallochaperone HypA from Helicobacter pylori~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Maroney, M]]~~	+	<div class="pdbe-citations 6g81" style="background-color:#fffaf0;"></div>
-	~~[[Category: Zambelli, B]]~~	+	== References ==
-	~~[[Category: Zerko, S]]~~	+	<references/>
-	[[Category: ~~Spronk~~, ~~C.A.E.M~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bardiaux, B]]
	[[Category: Ciurli, S]]		[[Category: Ciurli, S]]
		+	[[Category: Gorka, M]]
	[[Category: Hu, H]]		[[Category: Hu, H]]
-	[[Category: Piccioli, M]]
-	[[Category: Bardiaux, B]]
	[[Category: Kozminski, W]]		[[Category: Kozminski, W]]
-	[[Category: ~~Gorka~~, M]]	+	[[Category: Maroney, M]]
	[[Category: Musiani, F]]		[[Category: Musiani, F]]
		+	[[Category: Piccioli, M]]
		+	[[Category: Spronk, C A.E M]]
		+	[[Category: Zambelli, B]]
		+	[[Category: Zerko, S]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Metallochaperone metal-binding nickel hydrogenase]]

OCA at 06:00, 25 July 2018

OCA — Wed, 25 Jul 2018 06:00:26 GMT

←Older revision		Revision as of 06:00, 25 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6g81 is ON HOLD	+	The entry 6g81 is ON HOLD until Paper Publication

	Authors: Spronk, C.A.E.M., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Hu, H., Maroney, M., Ciurli, S.		Authors: Spronk, C.A.E.M., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Hu, H., Maroney, M., Ciurli, S.

OCA: Protected "6g81" [edit=sysop:move=sysop]

OCA — Wed, 18 Apr 2018 04:26:25 GMT

Protected "6g81" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:26, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6g81 is ON HOLD Authors: Spronk, C.A.E.M., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Hu, H., Maron...

OCA — Wed, 18 Apr 2018 04:26:23 GMT

New page: '''Unreleased structure''' The entry 6g81 is ON HOLD Authors: Spronk, C.A.E.M., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Hu, H., Maron...

New page

'''Unreleased structure'''

The entry 6g81 is ON HOLD

Authors: Spronk, C.A.E.M., Zerko, S., Gorka, M., Kozminski, W., Bardiaux, B., Zambelli, B., Musiani, F., Piccioli, M., Hu, H., Maroney, M., Ciurli, S.

Description: Solution structure of the Ni metallochaperone HypA from Helicobacter pylori
[[Category: Unreleased Structures]]
[[Category: Maroney, M]]
[[Category: Zambelli, B]]
[[Category: Zerko, S]]
[[Category: Spronk, C.A.E.M]]
[[Category: Ciurli, S]]
[[Category: Hu, H]]
[[Category: Piccioli, M]]
[[Category: Bardiaux, B]]
[[Category: Kozminski, W]]
[[Category: Gorka, M]]
[[Category: Musiani, F]]