5mdj - Revision history

OCA at 18:39, 1 November 2023

OCA — Wed, 01 Nov 2023 18:39:54 GMT

←Older revision		Revision as of 18:39, 1 November 2023
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	==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in a its as-isolated high-pressurized form==		==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in a its as-isolated high-pressurized form==
-	<StructureSection load='5mdj' size='340' side='right' caption='[[5mdj]], [[Resolution\|resolution]] 1.48Å' scene=''>	+	<StructureSection load='5mdj' size='340' side='right'caption='[[5mdj]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Alcaligenes_eutropha_h16 Alcaligenes eutropha h16~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator_H16 Cupriavidus necator H16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MDJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.48Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hoxG, PHG002 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16]), hoxK, PHG001 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </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=5mdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdj OCA], [https://pdbe.org/5mdj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mdj RCSB], [https://www.ebi.ac.uk/pdbsum/5mdj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdj 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=5mdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdj OCA], [~~http~~://pdbe.org/5mdj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mdj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mdj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. [[http://www.uniprot.org/uniprot/MBHS_CUPNH MBHS_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions.	+	[https://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcaligenes eutropha h16~~]]	+	[[Category: Cupriavidus necator H16]]
-	[[Category: ~~Kalms, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Scheerer, P~~]]	+	[[Category: Kalms J]]
-	[[Category: ~~Schmidt, A~~]]	+	[[Category: Scheerer P]]
-	[[Category: ~~Aerobic hydrogen bacteria]]~~	+	[[Category: Schmidt A]]
-	~~[[Category: As-isolated state]]~~	+
-	~~[[Category: Bimetallic]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Dihydrogen]]~~	+
-	~~[[Category: Fe-s cluster]]~~	+
-	~~[[Category: Gas transport]]~~	+
-	~~[[Category: High pressure cryo cooling]]~~	+
-	~~[[Category: High pressure pumping]]~~	+
-	~~[[Category: Hydrogen catalysis]]~~	+
-	~~[[Category: Hydrophobic tunnel]]~~	+
-	~~[[Category: Knallgasbacteria]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Membrane bound]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Metalloprotein catalytic center]]~~	+
-	~~[[Category: Ni-fe active site]]~~	+
-	~~[[Category: Oxidized state]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxygen tolerant hydrogenase]]~~	+
-	~~[[Category: Proteobacteria]]~~	+
-	~~[[Category: T-cluster~~]]	+

OCA at 06:57, 28 March 2018

OCA — Wed, 28 Mar 2018 06:57:55 GMT

←Older revision		Revision as of 06:57, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='5mdj' size='340' side='right' caption='[[5mdj]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='5mdj' size='340' side='right' caption='[[5mdj]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_eutropha_h16 Alcaligenes eutropha h16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hoxG, PHG002 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16]), hoxK, PHG001 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </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=5mdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdj OCA], [http://pdbe.org/5mdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdj RCSB], [http://www.ebi.ac.uk/pdbsum/5mdj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdj 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=5mdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdj OCA], [http://pdbe.org/5mdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdj RCSB], [http://www.ebi.ac.uk/pdbsum/5mdj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdj ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. [[http://www.uniprot.org/uniprot/MBHS_CUPNH MBHS_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions.		[[http://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. [[http://www.uniprot.org/uniprot/MBHS_CUPNH MBHS_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	[NiFe] hydrogenases catalyze the reversible splitting of H2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O2, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O2 to water. This O2 tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O2 attack. Here, the O2 accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O2 molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O2 concentrations used for MBH crystal derivatization. The examination of the O2-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O2 tolerance of the enzyme.
		+
		+	Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.,Kalms J, Schmidt A, Frielingsdorf S, Utesch T, Gotthard G, von Stetten D, van der Linden P, Royant A, Mroginski MA, Carpentier P, Lenz O, Scheerer P Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2229-E2237. doi:, 10.1073/pnas.1712267115. Epub 2018 Feb 20. PMID:29463722<ref>PMID:29463722</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5mdj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alcaligenes eutropha h16]]
	[[Category: Kalms, J]]		[[Category: Kalms, J]]
	[[Category: Scheerer, P]]		[[Category: Scheerer, P]]

OCA at 07:09, 22 February 2018

OCA — Thu, 22 Feb 2018 07:09:15 GMT

←Older revision		Revision as of 07:09, 22 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mdj is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in a its as-isolated high-pressurized form==
-		+	<StructureSection load='5mdj' size='340' side='right' caption='[[5mdj]], [[Resolution\|resolution]] 1.48Å' scene=''>
-	~~Authors~~: ~~Schmidt~~, A., ~~Kalms~~, J., ~~Scheerer~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5mdj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDJ FirstGlance]. <br>
-	~~Description~~: ~~crystal structure~~ of ~~oxygen tolerant, membrane bound~~ [~~NiFe~~] ~~hydrogenase~~ of ~~Ralstonia eutropha~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=F4S:FE4-S3+CLUSTER'>F4S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </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=5mdj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdj OCA], [http://pdbe.org/5mdj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdj RCSB], [http://www.ebi.ac.uk/pdbsum/5mdj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdj ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MBHL_CUPNH MBHL_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions. [[http://www.uniprot.org/uniprot/MBHS_CUPNH MBHS_CUPNH]] This enzyme recycles the H(2) produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O(2) under carbon- or phosphate-limited conditions.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kalms, J]]
	[[Category: Scheerer, P]]		[[Category: Scheerer, P]]
-	[[Category: Kalms, J]]
	[[Category: Schmidt, A]]		[[Category: Schmidt, A]]
		+	[[Category: Aerobic hydrogen bacteria]]
		+	[[Category: As-isolated state]]
		+	[[Category: Bimetallic]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Dihydrogen]]
		+	[[Category: Fe-s cluster]]
		+	[[Category: Gas transport]]
		+	[[Category: High pressure cryo cooling]]
		+	[[Category: High pressure pumping]]
		+	[[Category: Hydrogen catalysis]]
		+	[[Category: Hydrophobic tunnel]]
		+	[[Category: Knallgasbacteria]]
		+	[[Category: Membrane]]
		+	[[Category: Membrane bound]]
		+	[[Category: Metalloenzyme]]
		+	[[Category: Metalloprotein catalytic center]]
		+	[[Category: Ni-fe active site]]
		+	[[Category: Oxidized state]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxygen tolerant hydrogenase]]
		+	[[Category: Proteobacteria]]
		+	[[Category: T-cluster]]

OCA at 13:46, 4 January 2017

OCA — Wed, 04 Jan 2017 13:46:52 GMT

←Older revision		Revision as of 13:46, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5mdj is ON HOLD	+	The entry 5mdj is ON HOLD until Paper Publication

	Authors: Schmidt, A., Kalms, J., Scheerer, P.		Authors: Schmidt, A., Kalms, J., Scheerer, P.

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

OCA — Fri, 09 Dec 2016 16:40:52 GMT

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

←Older revision

Revision as of 16:40, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mdj is ON HOLD Authors: Schmidt, A., Kalms, J., Scheerer, P. Description: crystal structure of oxygen tolerant, membrane bound [NiFe] hydrogenase ...

OCA — Fri, 09 Dec 2016 16:40:51 GMT

New page: '''Unreleased structure''' The entry 5mdj is ON HOLD Authors: Schmidt, A., Kalms, J., Scheerer, P. Description: crystal structure of oxygen tolerant, membrane bound [NiFe] hydrogenase ...

New page

'''Unreleased structure'''

The entry 5mdj is ON HOLD

Authors: Schmidt, A., Kalms, J., Scheerer, P.

Description: crystal structure of oxygen tolerant, membrane bound [NiFe] hydrogenase of Ralstonia eutropha
[[Category: Unreleased Structures]]
[[Category: Scheerer, P]]
[[Category: Kalms, J]]
[[Category: Schmidt, A]]