5mdk - Revision history

OCA at 18:39, 1 November 2023

2023-11-01T18:39:54Z

←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 its as-isolated form (oxidized state - state 3)==		==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)==
-	<StructureSection load='5mdk' size='340' side='right' caption='[[5mdk]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5mdk' size='340' side='right'caption='[[5mdk]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdk]] 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=5MDK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdk]] 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=5MDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MDK 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]] 1.5Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HOXG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16]), HOXK ([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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [https://pdbe.org/5mdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [https://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk 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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [~~http~~://pdbe.org/5mdk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk 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: Hydrogen catalysis]]~~	+
-	~~[[Category: Hydrophobic tunnel]]~~	+
-	~~[[Category: Knallgasbacteria]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Membrane bound]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Metalloprotein catalytic center]]~~	+
-	~~[[Category: Native]]~~	+
-	~~[[Category: Ni-fe active site]]~~	+
-	~~[[Category: Oxidized state]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxygen tolerant hydrogenase]]~~	+
-	~~[[Category: Proteobacteria]]~~	+
-	~~[[Category: T-cluster~~]]	+

OCA at 06:58, 28 March 2018

2018-03-28T06:58:04Z

←Older revision		Revision as of 06:58, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='5mdk' size='340' side='right' caption='[[5mdk]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5mdk' size='340' side='right' caption='[[5mdk]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdk]] 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=5MDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDK 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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381666 Alcaligenes eutropha H16]), HOXK ([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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [http://pdbe.org/5mdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [http://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk 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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [http://pdbe.org/5mdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [http://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk 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 5mdk" 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

2018-02-22T07:09:40Z

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

-	~~The entry~~ 5mdk is ~~ON HOLD~~	+	==Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)==
-		+	<StructureSection load='5mdk' size='340' side='right' caption='[[5mdk]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~: ~~Schmidt~~, A., ~~Kalms~~, J., ~~Scheerer~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5mdk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDK 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=5mdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdk OCA], [http://pdbe.org/5mdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdk RCSB], [http://www.ebi.ac.uk/pdbsum/5mdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdk 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: Hydrogen catalysis]]
		+	[[Category: Hydrophobic tunnel]]
		+	[[Category: Knallgasbacteria]]
		+	[[Category: Membrane]]
		+	[[Category: Membrane bound]]
		+	[[Category: Metalloenzyme]]
		+	[[Category: Metalloprotein catalytic center]]
		+	[[Category: Native]]
		+	[[Category: Ni-fe active site]]
		+	[[Category: Oxidized state]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxygen tolerant hydrogenase]]
		+	[[Category: Proteobacteria]]
		+	[[Category: T-cluster]]

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

2016-12-09T16:40:55Z

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

←Older revision

Revision as of 16:40, 9 December 2016

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

2016-12-09T16:40:54Z

New page: '''Unreleased structure''' The entry 5mdk 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 5mdk 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]]