8pow - Revision history

OCA: Replacing page with ''''Unreleased structure''' The entry 8pow is ON HOLD until Paper Publication Authors: Kalms, J., Schmidt, A., Scheerer, P. Description: Crystal Structure of the C19G varian...'

2023-11-22T05:38:21Z

Replacing page with ''''Unreleased structure''' The entry 8pow is ON HOLD until Paper Publication Authors: Kalms, J., Schmidt, A., Scheerer, P. Description: Crystal Structure of the C19G varian...'

←Older revision		Revision as of 05:38, 22 November 2023
Line 1:		Line 1:
		+	'''Unreleased structure'''

-	~~==Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.==~~	+	The entry 8pow is ON HOLD until Paper Publication
-	~~<StructureSection load='~~8pow~~' size='340' side='right'caption='[[8pow]], [[Resolution\|resolution]] 1.61Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[8pow]]~~ 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=8POW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8POW FirstGlance]. <br>	+
-	~~</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.61Å</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=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=ER2:Fe4S4'>ER2</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8pow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pow OCA], [https://pdbe.org/8pow PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pow RCSB], [https://www.ebi.ac.uk/pdbsum/8pow PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pow ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	[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;">~~	+
-	== Publication ~~Abstract from PubMed ==~~	+
-	The membrane-bound [NiFe]-hydrogenase of Cupriavidus necator is a rare example of a truly O(2)-tolerant hydrogenase. It catalyzes the oxidation of H(2) into 2e(-) and 2H(+) in the presence of high O(2) concentrations. This characteristic trait is intimately linked to the unique Cys(6)[4Fe-3S] cluster located in the proximal position to the catalytic center and coordinated by six cysteine residues. Two of these cysteines play an essential role in redox-dependent cluster plasticity, which bestows the cofactor with the capacity to mediate two redox transitions at physiological potentials. Here, we investigated the individual roles of the two additional cysteines by replacing them individually as well as simultaneously with glycine. The crystal structures of the corresponding MBH variants revealed the presence of Cys(5)[4Fe-4S] or Cys(4)[4Fe-4S] clusters of different architecture. The protein X-ray crystallography results were correlated with accompanying biochemical, spectroscopic and electrochemical data. The exchanges resulted in a diminished O(2) tolerance of all MBH variants, which was attributed to the fact that the modified proximal clusters mediated only one redox transition. The previously proposed O(2) protection mechanism that detoxifies O(2) to H(2)O using four protons and four electrons supplied by the cofactor infrastructure, is extended by our results, which suggest efficient shutdown of enzyme function by formation of a hydroxy ligand in the active site that protects the enzyme from O(2) binding under electron-deficient conditions.	+

-	~~Stepwise conversion of the Cys(6)[4Fe-3S] to a Cys(4)[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase.,Schmidt A,~~ Kalms ~~J, Lorent C, Katz S, Frielingsdorf S, Evans RM~~, ~~Fritsch~~ J, ~~Siebert E~~, ~~Teutloff C~~, ~~Armstrong FA~~, ~~Zebger I, Lenz O, Scheerer~~ P ~~Chem Sci~~. ~~2023 Sep 20;14(40):11105-11120. doi: 10.1039/d3sc03739h. eCollection , 2023 Oct 18. PMID:37860641<ref>PMID:37860641</ref>~~	+	Authors: Kalms, J., Schmidt, A., Scheerer, P.

-	~~From MEDLINE®/PubMed®, a database~~ of the ~~U.S. National Library~~ of ~~Medicine.<br>~~	+	Description: Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.
-	~~</div>~~	+	[[Category: Unreleased Structures]]
-	~~<div class="pdbe~~-~~citations 8pow" style="background~~-~~color:#fffaf0;"></div>~~	+	[[Category: Kalms, J]]
-	~~== References ==~~	+	[[Category: Schmidt, A]]
-	~~<references/>~~	+	[[Category: Scheerer, P]]
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category:~~ Cupriavidus necator ~~H16]]~~	+
-	[[Category: ~~Large~~ Structures]]	+
-	[[Category: Kalms J]]	+
-	[[Category: ~~Scheerer P~~]]	+
-	[[Category: ~~Schmidt A~~]]	+

OCA at 07:40, 15 November 2023

2023-11-15T07:40:20Z

←Older revision		Revision as of 07:40, 15 November 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8pow is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.==
		+	<StructureSection load='8pow' size='340' side='right'caption='[[8pow]], [[Resolution\|resolution]] 1.61Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8pow]] 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=8POW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8POW FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.61Å</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=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=ER2:Fe4S4'>ER2</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8pow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pow OCA], [https://pdbe.org/8pow PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pow RCSB], [https://www.ebi.ac.uk/pdbsum/8pow PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pow ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[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;">
		+	== Publication Abstract from PubMed ==
		+	The membrane-bound [NiFe]-hydrogenase of Cupriavidus necator is a rare example of a truly O(2)-tolerant hydrogenase. It catalyzes the oxidation of H(2) into 2e(-) and 2H(+) in the presence of high O(2) concentrations. This characteristic trait is intimately linked to the unique Cys(6)[4Fe-3S] cluster located in the proximal position to the catalytic center and coordinated by six cysteine residues. Two of these cysteines play an essential role in redox-dependent cluster plasticity, which bestows the cofactor with the capacity to mediate two redox transitions at physiological potentials. Here, we investigated the individual roles of the two additional cysteines by replacing them individually as well as simultaneously with glycine. The crystal structures of the corresponding MBH variants revealed the presence of Cys(5)[4Fe-4S] or Cys(4)[4Fe-4S] clusters of different architecture. The protein X-ray crystallography results were correlated with accompanying biochemical, spectroscopic and electrochemical data. The exchanges resulted in a diminished O(2) tolerance of all MBH variants, which was attributed to the fact that the modified proximal clusters mediated only one redox transition. The previously proposed O(2) protection mechanism that detoxifies O(2) to H(2)O using four protons and four electrons supplied by the cofactor infrastructure, is extended by our results, which suggest efficient shutdown of enzyme function by formation of a hydroxy ligand in the active site that protects the enzyme from O(2) binding under electron-deficient conditions.

-	~~Authors:~~ Kalms, J., ~~Schmidt~~, A., ~~Scheerer~~, P.	+	Stepwise conversion of the Cys(6)[4Fe-3S] to a Cys(4)[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase.,Schmidt A, Kalms J, Lorent C, Katz S, Frielingsdorf S, Evans RM, Fritsch J, Siebert E, Teutloff C, Armstrong FA, Zebger I, Lenz O, Scheerer P Chem Sci. 2023 Sep 20;14(40):11105-11120. doi: 10.1039/d3sc03739h. eCollection , 2023 Oct 18. PMID:37860641<ref>PMID:37860641</ref>

-	~~Description: Crystal Structure~~ of the ~~C19G variant~~ of ~~the membrane~~-~~bound [NiFe]~~-~~Hydrogenase from~~ Cupriavidus necator ~~in the air-oxidized state at 1.61 A Resolution.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Scheerer, P~~]]	+	<div class="pdbe-citations 8pow" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kalms, J~~]]	+	== References ==
-	[[Category: Schmidt, A]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cupriavidus necator H16]]
		+	[[Category: Large Structures]]
		+	[[Category: Kalms J]]
		+	[[Category: Scheerer P]]
		+	[[Category: Schmidt A]]

OCA at 04:41, 23 August 2023

2023-08-23T04:41:12Z

←Older revision		Revision as of 04:41, 23 August 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8pow is ON HOLD	+	The entry 8pow is ON HOLD until Paper Publication

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

OCA: Protected "8pow" [edit=sysop:move=sysop]

2023-07-12T04:26:29Z

Protected "8pow" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:26, 12 July 2023

OCA: New page: '''Unreleased structure''' The entry 8pow is ON HOLD Authors: Kalms, J., Schmidt, A., Scheerer, P. Description: Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydro...

2023-07-12T04:26:27Z

New page: '''Unreleased structure''' The entry 8pow is ON HOLD Authors: Kalms, J., Schmidt, A., Scheerer, P. Description: Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydro...

New page

'''Unreleased structure'''

The entry 8pow is ON HOLD

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

Description: Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.
[[Category: Unreleased Structures]]
[[Category: Scheerer, P]]
[[Category: Kalms, J]]
[[Category: Schmidt, A]]