5jsy - Revision history

OCA at 19:04, 20 September 2023

OCA — Wed, 20 Sep 2023 19:04:54 GMT

←Older revision		Revision as of 19:04, 20 September 2023
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	<StructureSection load='5jsy' size='340' side='right'caption='[[5jsy]], [[Resolution\|resolution]] 1.04Å' scene=''>		<StructureSection load='5jsy' size='340' side='right'caption='[[5jsy]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jsy]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Desvh Desvh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JSY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jsy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JSY FirstGlance]. <br>
-	</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=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.04Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>~~</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=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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">hysB~~, DVU_1917 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH]), hysA, DVU_1918 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])<~~/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=5jsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsy OCA], [https://pdbe.org/5jsy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jsy RCSB], [https://www.ebi.ac.uk/pdbsum/5jsy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsy ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:</~~b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2]~~ </~~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=5jsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsy OCA], [~~http~~://pdbe.org/5jsy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jsy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jsy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsy ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72AS4_DESVH Q72AS4_DESVH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desvh]]~~	+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
-	~~[[Category: Ferredoxin hydrogenase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Marques~~, M C~~]]	+	[[Category: Marques MC]]
-	[[Category: Matias~~, P M~~]]	+	[[Category: Matias PM]]
-	[[Category: Pereira~~, I A.C]]~~	+	[[Category: Pereira IAC]]
-	~~[[Category: Nifese-site h2 cleavage/production]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:37, 17 June 2020

OCA — Wed, 17 Jun 2020 11:37:03 GMT

←Older revision		Revision as of 11:37, 17 June 2020
Line 1:		Line 1:

	==The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution==		==The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution==
-	<StructureSection load='5jsy' size='340' side='right' caption='[[5jsy]], [[Resolution\|resolution]] 1.04Å' scene=''>	+	<StructureSection load='5jsy' size='340' side='right'caption='[[5jsy]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jsy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JSY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jsy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JSY 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=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hysB, DVU_1917 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH]), hysA, DVU_1918 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </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=5jsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsy OCA], [http://pdbe.org/5jsy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jsy RCSB], [http://www.ebi.ac.uk/pdbsum/5jsy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsy 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=5jsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsy OCA], [http://pdbe.org/5jsy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jsy RCSB], [http://www.ebi.ac.uk/pdbsum/5jsy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Desvh]]
	[[Category: Ferredoxin hydrogenase]]		[[Category: Ferredoxin hydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Marques, M C]]		[[Category: Marques, M C]]
	[[Category: Matias, P M]]		[[Category: Matias, P M]]

OCA at 06:17, 4 May 2017

OCA — Thu, 04 May 2017 06:17:18 GMT

←Older revision		Revision as of 06:17, 4 May 2017
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	<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=5jsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsy OCA], [http://pdbe.org/5jsy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jsy RCSB], [http://www.ebi.ac.uk/pdbsum/5jsy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsy 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=5jsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsy OCA], [http://pdbe.org/5jsy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jsy RCSB], [http://www.ebi.ac.uk/pdbsum/5jsy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrogenases are highly active enzymes for hydrogen production and oxidation. [NiFeSe] hydrogenases, in which selenocysteine is a ligand to the active site Ni, have high catalytic activity and a bias for H2 production. In contrast to [NiFe] hydrogenases, they display reduced H2 inhibition and are rapidly reactivated after contact with oxygen. Here we report an expression system for production of recombinant [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough and study of a selenocysteine-to-cysteine variant (Sec489Cys) in which, for the first time, a [NiFeSe] hydrogenase was converted to a [NiFe] type. This modification led to severely reduced Ni incorporation, revealing the direct involvement of this residue in the maturation process. The Ni-depleted protein could be partly reconstituted to generate an enzyme showing much lower activity and inactive states characteristic of [NiFe] hydrogenases. The Ni-Sec489Cys variant shows that selenium has a crucial role in protection against oxidative damage and the high catalytic activities of the [NiFeSe] hydrogenases.
		+
		+	The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis.,Marques MC, Tapia C, Gutierrez-Sanz O, Ramos AR, Keller KL, Wall JD, De Lacey AL, Matias PM, Pereira IAC Nat Chem Biol. 2017 May;13(5):544-550. doi: 10.1038/nchembio.2335. Epub 2017 Mar , 20. PMID:28319099<ref>PMID:28319099</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jsy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:22, 22 March 2017

OCA — Wed, 22 Mar 2017 16:22:04 GMT

←Older revision		Revision as of 16:22, 22 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5jsy is ON HOLD until Paper Publication~~	+	==The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution==
-		+	<StructureSection load='5jsy' size='340' side='right' caption='[[5jsy]], [[Resolution\|resolution]] 1.04Å' scene=''>
-	~~Authors: Marques, M.C., Pereira, I.A.C., Matias, P.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jsy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JSY FirstGlance]. <br>
-	~~Description:~~ The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution	+	</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=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
-	[[Category: Marques, M.C]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>
-	[[Category: Pereira, I.A.C]]	+	<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=5jsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jsy OCA], [http://pdbe.org/5jsy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jsy RCSB], [http://www.ebi.ac.uk/pdbsum/5jsy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jsy ProSAT]</span></td></tr>
-	[[Category: ~~Matias, P.M~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ferredoxin hydrogenase]]
		+	[[Category: Marques, M C]]
		+	[[Category: Matias, P M]]
		+	[[Category: Pereira, I A.C]]
		+	[[Category: Nifese-site h2 cleavage/production]]
		+	[[Category: Oxidoreductase]]

OCA at 10:01, 9 March 2017

OCA — Thu, 09 Mar 2017 10:01:21 GMT

←Older revision		Revision as of 10:01, 9 March 2017
Line 7:		Line 7:
	Description: The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution		Description: The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Pereira, I.A.C]]
	[[Category: Marques, M.C]]		[[Category: Marques, M.C]]
		+	[[Category: Pereira, I.A.C]]
	[[Category: Matias, P.M]]		[[Category: Matias, P.M]]

OCA at 23:39, 12 July 2016

OCA — Tue, 12 Jul 2016 23:39:28 GMT

←Older revision		Revision as of 23:39, 12 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Marques, M.C., Pereira, I.A.C., Matias, P.M.		Authors: Marques, M.C., Pereira, I.A.C., Matias, P.M.

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

OCA — Wed, 01 Jun 2016 13:47:39 GMT

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

←Older revision

Revision as of 13:47, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jsy is ON HOLD Authors: Marques, M.C., Pereira, I.A.C., Matias, P.M. Description: The 3D structure of the Ni-reconstituted U489C variant of [NiFeS...

OCA — Wed, 01 Jun 2016 13:47:37 GMT

New page: '''Unreleased structure''' The entry 5jsy is ON HOLD Authors: Marques, M.C., Pereira, I.A.C., Matias, P.M. Description: The 3D structure of the Ni-reconstituted U489C variant of [NiFeS...

New page

'''Unreleased structure'''

The entry 5jsy is ON HOLD

Authors: Marques, M.C., Pereira, I.A.C., Matias, P.M.

Description: The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution
[[Category: Unreleased Structures]]
[[Category: Pereira, I.A.C]]
[[Category: Marques, M.C]]
[[Category: Matias, P.M]]