3usc - Revision history

OCA at 10:27, 1 March 2024

2024-03-01T10:27:19Z

←Older revision		Revision as of 10:27, 1 March 2024
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	<StructureSection load='3usc' size='340' side='right'caption='[[3usc]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3usc' size='340' side='right'caption='[[3usc]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3usc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3USC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3usc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3USC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3uqy\|3uqy]], [[3use\|3use]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0972, hyaA, JW0954 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), b0973, hyaB, JW0955 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [https://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=3usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3usc OCA], [https://pdbe.org/3usc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3usc RCSB], [https://www.ebi.ac.uk/pdbsum/3usc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3usc ProSAT]</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=3usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3usc OCA], [https://pdbe.org/3usc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3usc RCSB], [https://www.ebi.ac.uk/pdbsum/3usc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3usc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MBHS_ECOLI MBHS_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth. [[https://www.uniprot.org/uniprot/MBHL_ECOLI MBHL_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth.	+	[https://www.uniprot.org/uniprot/MBHS_ECOLI MBHS_ECOLI] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The crystal structure of the membrane-bound O(2)-tolerant [NiFe]-hydrogenase 1 from Escherichia coli (EcHyd-1) has been solved in three different states: as-isolated, H(2)-reduced, and chemically oxidized. As very recently reported for similar enzymes from Ralstonia eutropha and Hydrogenovibrio marinus, two supernumerary Cys residues coordinate the proximal [FeS] cluster in EcHyd-1, which lacks one of the inorganic sulfide ligands. We find that the as-isolated, aerobically purified species contains a mixture of at least two conformations for one of the cluster iron ions and Glu76. In one of them, Glu76 and the iron occupy positions that are similar to those found in O(2)-sensitive [NiFe]-hydrogenases. In the other conformation, this iron binds, besides three sulfur ligands, the amide N from Cys20 and one Oepsilon of Glu76. Our calculations show that oxidation of this unique iron generates the high-potential form of the proximal cluster. The structural rearrangement caused by oxidation is confirmed by our H(2)-reduced and oxidized EcHyd-1 structures. Thus, thanks to the peculiar coordination of the unique iron, the proximal cluster can contribute two successive electrons to secure complete reduction of O(2) to H(2)O at the active site. The two observed conformations of Glu76 are consistent with this residue playing the role of a base to deprotonate the amide moiety of Cys20 upon iron binding and transfer the resulting proton away, thus allowing the second oxidation to be electroneutral. The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O(2) reduction, located near the active site.	+
-		+
-	X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.,Volbeda A, Amara P, Darnault C, Mouesca JM, Parkin A, Roessler MM, Armstrong FA, Fontecilla-Camps JC Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5305-10. Epub 2012 Mar 19. PMID:22431599<ref>PMID:22431599</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3usc" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Darnault, C]]	+	[[Category: Darnault C]]
-	[[Category: Fontecilla-Camps~~, J C~~]]	+	[[Category: Fontecilla-Camps JC]]
-	[[Category: Volbeda, A]]	+	[[Category: Volbeda A]]
-	~~[[Category: Membrane-bound hydrogenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:02, 20 July 2022

2022-07-20T08:02:24Z

←Older revision		Revision as of 08:02, 20 July 2022
Line 1:		Line 1:

	==Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form==		==Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form==
-	<StructureSection load='3usc' size='340' side='right' caption='[[3usc]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3usc' size='340' side='right'caption='[[3usc]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3usc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3USC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3usc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3USC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uqy\|3uqy]], [[3use\|3use]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3uqy\|3uqy]], [[3use\|3use]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0972, hyaA, JW0954 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), b0973, hyaB, JW0955 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0972, hyaA, JW0954 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), b0973, hyaB, JW0955 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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'>[https://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [https://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=3usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3usc OCA], [~~http~~://pdbe.org/3usc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3usc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3usc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3usc ProSAT]</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=3usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3usc OCA], [https://pdbe.org/3usc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3usc RCSB], [https://www.ebi.ac.uk/pdbsum/3usc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3usc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MBHS_ECOLI MBHS_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth. [[~~http~~://www.uniprot.org/uniprot/MBHL_ECOLI MBHL_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth.	+	[[https://www.uniprot.org/uniprot/MBHS_ECOLI MBHS_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth. [[https://www.uniprot.org/uniprot/MBHL_ECOLI MBHL_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Darnault, C]]		[[Category: Darnault, C]]
	[[Category: Fontecilla-Camps, J C]]		[[Category: Fontecilla-Camps, J C]]

OCA at 16:38, 11 August 2016

2016-08-11T16:38:26Z

←Older revision		Revision as of 16:38, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form==		==Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form==
	<StructureSection load='3usc' size='340' side='right' caption='[[3usc]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3usc' size='340' side='right' caption='[[3usc]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3USC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3USC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uqy\|3uqy]], [[3use\|3use]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uqy\|3uqy]], [[3use\|3use]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0972, hyaA, JW0954 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), b0973, hyaB, JW0955 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0972, hyaA, JW0954 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), b0973, hyaB, JW0955 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3usc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3usc RCSB], [http://www.ebi.ac.uk/pdbsum/3usc PDBsum]</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=3usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3usc OCA], [http://pdbe.org/3usc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3usc RCSB], [http://www.ebi.ac.uk/pdbsum/3usc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3usc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MBHS_ECOLI MBHS_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth. [[http://www.uniprot.org/uniprot/MBHL_ECOLI MBHL_ECOLI]] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD1 is believed to have a role in hydrogen cycling during fermentative growth.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3usc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Darnault, C]]		[[Category: Darnault, C]]
	[[Category: Fontecilla-Camps, J C]]		[[Category: Fontecilla-Camps, J C]]

OCA at 10:03, 4 January 2015

2015-01-04T10:03:53Z

←Older revision		Revision as of 10:03, 4 January 2015
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-	[[~~Image:~~3usc.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form==
		+	<StructureSection load='3usc' size='340' side='right' caption='[[3usc]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3USC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NI:NICKEL+(III)+ION'>3NI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF3:FE4-S3+CLUSTER'>SF3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3uqy\|3uqy]], [[3use\|3use]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0972, hyaA, JW0954 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), b0973, hyaB, JW0955 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3usc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3usc RCSB], [http://www.ebi.ac.uk/pdbsum/3usc PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the membrane-bound O(2)-tolerant [NiFe]-hydrogenase 1 from Escherichia coli (EcHyd-1) has been solved in three different states: as-isolated, H(2)-reduced, and chemically oxidized. As very recently reported for similar enzymes from Ralstonia eutropha and Hydrogenovibrio marinus, two supernumerary Cys residues coordinate the proximal [FeS] cluster in EcHyd-1, which lacks one of the inorganic sulfide ligands. We find that the as-isolated, aerobically purified species contains a mixture of at least two conformations for one of the cluster iron ions and Glu76. In one of them, Glu76 and the iron occupy positions that are similar to those found in O(2)-sensitive [NiFe]-hydrogenases. In the other conformation, this iron binds, besides three sulfur ligands, the amide N from Cys20 and one Oepsilon of Glu76. Our calculations show that oxidation of this unique iron generates the high-potential form of the proximal cluster. The structural rearrangement caused by oxidation is confirmed by our H(2)-reduced and oxidized EcHyd-1 structures. Thus, thanks to the peculiar coordination of the unique iron, the proximal cluster can contribute two successive electrons to secure complete reduction of O(2) to H(2)O at the active site. The two observed conformations of Glu76 are consistent with this residue playing the role of a base to deprotonate the amide moiety of Cys20 upon iron binding and transfer the resulting proton away, thus allowing the second oxidation to be electroneutral. The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O(2) reduction, located near the active site.

-	~~{{STRUCTURE_3usc\| PDB=3usc \| SCENE= }}~~	+	X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.,Volbeda A, Amara P, Darnault C, Mouesca JM, Parkin A, Roessler MM, Armstrong FA, Fontecilla-Camps JC Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5305-10. Epub 2012 Mar 19. PMID:22431599<ref>PMID:22431599</ref>

-	~~===Crystal Structure~~ of E. ~~coli hydrogenase-1 in a ferricyanide-oxidized form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22431599}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3usc]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].~~	+	</StructureSection>
-		+
-	==~~See Also==~~	+
-	*[[Ribosomal protein S1\|Ribosomal protein S1]]	+
-		+
-	~~==Reference~~==	+
-	<~~ref group="xtra">PMID:022431599<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Darnault, C.]]	+	[[Category: Darnault, C]]
-	[[Category: Fontecilla-Camps, J C.]]	+	[[Category: Fontecilla-Camps, J C]]
-	[[Category: Volbeda, A.]]	+	[[Category: Volbeda, A]]
	[[Category: Membrane-bound hydrogenase]]		[[Category: Membrane-bound hydrogenase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 21:03, 20 October 2012

2012-10-20T21:03:19Z

←Older revision		Revision as of 21:03, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3usc]] is a 4 chain structure ~~of [[Ribosomal protein S1]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].	+	[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].

	==See Also==		==See Also==

OCA at 12:27, 27 July 2012

2012-07-27T12:27:19Z

←Older revision		Revision as of 12:27, 27 July 2012
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	[[Image:3usc.png\|left\|200px]]		[[Image:3usc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3usc", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3usc\| PDB=3usc \| SCENE= }}		{{STRUCTURE_3usc\| PDB=3usc \| SCENE= }}

	===Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form===		===Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22431599}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22431599 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22431599}}		{{ABSTRACT_PUBMED_22431599}}

	==About this Structure==		==About this Structure==
-	[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].	+	[[3usc]] is a 4 chain structure of [[Ribosomal protein S1]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].
		+
		+	==See Also==
		+	*[[Ribosomal protein S1\|Ribosomal protein S1]]

	==Reference==		==Reference==

OCA at 06:56, 18 April 2012

2012-04-18T06:56:52Z

←Older revision		Revision as of 06:56, 18 April 2012
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-	[[Image:3usc.~~jpg~~\|left\|200px]]	+	[[Image:3usc.png\|left\|200px]]

	<!--		<!--
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	===Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form===		===Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22431599}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22431599 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22431599}}

	==About this Structure==		==About this Structure==
	[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].		[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022431599</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Darnault, C.]]		[[Category: Darnault, C.]]

OCA at 07:51, 28 March 2012

2012-03-28T07:51:00Z

←Older revision		Revision as of 07:51, 28 March 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:3usc.jpg\|left\|200px]]

-	The ~~entry 3usc~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3usc", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3usc\| PDB=3usc \| SCENE= }}

-	~~Authors: Volbeda, A~~.~~, Fontecilla~~-~~Camps, J.C., Darnault, C.~~	+	===Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form===

-	~~Description: Crystal~~ Structure ~~of E~~. coli ~~hydrogenase~~-~~1 in a ferricyanide~~-~~oxidized form~~	+
		+	==About this Structure==
		+	[[3usc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3USC OCA].
		+	[[Category: Escherichia coli]]
		+	[[Category: Darnault, C.]]
		+	[[Category: Fontecilla-Camps, J C.]]
		+	[[Category: Volbeda, A.]]
		+	[[Category: Membrane-bound hydrogenase]]
		+	[[Category: Oxidoreductase]]

OCA at 05:17, 8 March 2012

2012-03-08T05:17:39Z

←Older revision		Revision as of 05:17, 8 March 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3usc is ON HOLD	+	The entry 3usc is ON HOLD until Paper Publication

	Authors: Volbeda, A., Fontecilla-Camps, J.C., Darnault, C.		Authors: Volbeda, A., Fontecilla-Camps, J.C., Darnault, C.

	Description: Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form		Description: Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form

OCA: Protected "3usc" [edit=sysop:move=sysop]

2011-11-30T05:56:42Z

Protected "3usc" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:56, 30 November 2011