5xlg - Revision history

OCA at 06:53, 14 October 2020

OCA — Wed, 14 Oct 2020 06:53:42 GMT

←Older revision		Revision as of 06:53, 14 October 2020
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	==Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase==		==Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase==
-	<StructureSection load='5xlg' size='340' side='right' caption='[[5xlg]], [[Resolution\|resolution]] 1.64Å' scene=''>	+	<StructureSection load='5xlg' size='340' side='right'caption='[[5xlg]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xlg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_(strain_miyazaki_f_/_dsm_19637) Desulfovibrio vulgaris (strain miyazaki f / dsm 19637)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XLG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XLG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xlg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_(strain_miyazaki_f_/_dsm_19637) Desulfovibrio vulgaris (strain miyazaki f / dsm 19637)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XLG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XLG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c3_hydrogenase Cytochrome-c3 hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.2.1 1.12.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c3_hydrogenase Cytochrome-c3 hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.2.1 1.12.2.1] </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=5xlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xlg OCA], [http://pdbe.org/5xlg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xlg RCSB], [http://www.ebi.ac.uk/pdbsum/5xlg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xlg ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xlg OCA], [http://pdbe.org/5xlg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xlg RCSB], [http://www.ebi.ac.uk/pdbsum/5xlg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xlg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Cytochrome-c3 hydrogenase]]		[[Category: Cytochrome-c3 hydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Hiromoto, T]]		[[Category: Hiromoto, T]]

OCA at 05:50, 6 June 2018

OCA — Wed, 06 Jun 2018 05:50:32 GMT

←Older revision		Revision as of 05:50, 6 June 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5xlg is ~~ON HOLD until Jun 14 2019~~	+	==Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase==
		+	<StructureSection load='5xlg' size='340' side='right' caption='[[5xlg]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xlg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_(strain_miyazaki_f_/_dsm_19637) Desulfovibrio vulgaris (strain miyazaki f / dsm 19637)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XLG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XLG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c3_hydrogenase Cytochrome-c3 hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.2.1 1.12.2.1] </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=5xlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xlg OCA], [http://pdbe.org/5xlg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xlg RCSB], [http://www.ebi.ac.uk/pdbsum/5xlg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xlg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PHNS_DESVM PHNS_DESVM]] Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. [[http://www.uniprot.org/uniprot/PHNL_DESVM PHNL_DESVM]] Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrogenase is a key enzyme for a coming hydrogen energy society, because it has strong catalytic activities on both uptake and production of dihydrogen. We, however, have to overcome the sensitivity against O2 of the enzyme, because hydrogenase is, generally, easily inactivated in the presence of O2. In this study, we have revisited the crystal structures of [NiFe]hydrogenase from sulfate-reducing bacterium in the several oxidized and reduced conditions. Our results revealed that the Ni-Fe active site of the enzyme exposed into O2 showed two forms, Form-1 and Form-2. The Ni-Fe active site in Form-1 showed the typical Ni-B (inactive ready) structure, whereas those in Form-2 lost Ni with no relation to an exposure time to O2, and two cysteinyl sulfur ligands made a disulfide bond. On the other hand, the formation of sulfenylation of the cysteinyl ligand to Ni, which is often observed in the oxidized form, did not correlate with the Ni-elimination, but with exposure time to O2.

-	~~Authors: Nishikawa~~, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.	+	Ni-elimination from the active site of the standard [NiFe]hydrogenase upon oxidation by O2.,Nishikawa K, Mochida S, Hiromoto T, Shibata N, Higuchi Y J Inorg Biochem. 2017 Dec;177:435-437. doi: 10.1016/j.jinorgbio.2017.09.011. Epub, 2017 Sep 14. PMID:28967475<ref>PMID:28967475</ref>

-	~~Description: Crystal structure~~ of ~~anaerobically purified and aerobically crystallized D~~. ~~vulgaris Miyazaki F [NiFe]~~-~~hydrogenase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Mochida~~, S]]	+	<div class="pdbe-citations 5xlg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cytochrome-c3 hydrogenase]]
		+	[[Category: Higuchi, Y]]
	[[Category: Hiromoto, T]]		[[Category: Hiromoto, T]]
		+	[[Category: Mochida, S]]
	[[Category: Nishikawa, K]]		[[Category: Nishikawa, K]]
	[[Category: Shibata, N]]		[[Category: Shibata, N]]
-	[[Category: ~~Higuchi, Y~~]]	+	[[Category: Oxidoreductase]]

OCA at 03:47, 16 May 2018

OCA — Wed, 16 May 2018 03:47:03 GMT

←Older revision		Revision as of 03:47, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xlg is ON HOLD	+	The entry 5xlg is ON HOLD until Jun 14 2019

	Authors: Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.		Authors: Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.
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	Description: Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase		Description: Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Nishikawa, K]]
-	[[Category: Higuchi, Y]]
	[[Category: Mochida, S]]		[[Category: Mochida, S]]
	[[Category: Hiromoto, T]]		[[Category: Hiromoto, T]]
		+	[[Category: Nishikawa, K]]
	[[Category: Shibata, N]]		[[Category: Shibata, N]]
		+	[[Category: Higuchi, Y]]

OCA at 15:33, 27 September 2017

OCA — Wed, 27 Sep 2017 15:33:03 GMT

←Older revision		Revision as of 15:33, 27 September 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Nishikawa, K]]		[[Category: Nishikawa, K]]
-	[[Category: Shibata, N]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Mochida, S]]		[[Category: Mochida, S]]
	[[Category: Hiromoto, T]]		[[Category: Hiromoto, T]]
		+	[[Category: Shibata, N]]

OCA at 12:35, 24 May 2017

OCA — Wed, 24 May 2017 12:35:11 GMT

←Older revision		Revision as of 12:35, 24 May 2017
Line 3:		Line 3:
	The entry 5xlg is ON HOLD		The entry 5xlg is ON HOLD

-	Authors: Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y	+	Authors: Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.

	Description: Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase		Description: Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Nishikawa, K, Mochida, S, Hiromoto, T~~, Shibata, N, Higuchi, Y~~]]	+	[[Category: Nishikawa, K]]
		+	[[Category: Shibata, N]]
		+	[[Category: Higuchi, Y]]
		+	[[Category: Mochida, S]]
		+	[[Category: Hiromoto, T]]

OCA: Protected "5xlg" [edit=sysop:move=sysop]

OCA — Wed, 17 May 2017 14:55:33 GMT

Protected "5xlg" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:55, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5xlg is ON HOLD Authors: Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y Description: Crystal structure of anaerobically purified and...

OCA — Wed, 17 May 2017 14:55:31 GMT

New page: '''Unreleased structure''' The entry 5xlg is ON HOLD Authors: Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y Description: Crystal structure of anaerobically purified and...

New page

'''Unreleased structure'''

The entry 5xlg is ON HOLD

Authors: Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y

Description: Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase
[[Category: Unreleased Structures]]
[[Category: Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y]]