6gal - Revision history

OCA at 06:20, 10 July 2019

2019-07-10T06:20:49Z

←Older revision		Revision as of 06:20, 10 July 2019
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	==Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10==		==Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10==
-	<StructureSection load='6gal' size='340' side='right' caption='[[6gal]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='6gal' size='340' side='right'caption='[[6gal]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6gal]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ ~~] and [http://en.wikipedia.org/wiki/Escherichia_coli_(strain_k12) Escherichia coli (strain k12)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GAL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GAL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6gal]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GAL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GAL 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=CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC+ACID'>CXS</scene>, <scene name='pdbligand=EJ2:NI-FE+REDUCED+ACTIVE+CENTER'>EJ2</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC+ACID'>CXS</scene>, <scene name='pdbligand=EJ2:NI-FE+REDUCED+ACTIVE+CENTER'>EJ2</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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">[[6fpw\|6fpw]], [[6fpi\|6fpi]], [[6g7r\|6g7r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6fpw\|6fpw]], [[6fpi\|6fpi]], [[6g7r\|6g7r]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hyaA, b0972, JW0954 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6gal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gal OCA], [http://pdbe.org/6gal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gal RCSB], [http://www.ebi.ac.uk/pdbsum/6gal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gal 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=6gal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gal OCA], [http://pdbe.org/6gal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gal RCSB], [http://www.ebi.ac.uk/pdbsum/6gal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gal ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Armstrong, F A]]		[[Category: Armstrong, F A]]
	[[Category: Carr, S B]]		[[Category: Carr, S B]]

OCA at 15:19, 27 February 2019

2019-02-27T15:19:40Z

←Older revision		Revision as of 15:19, 27 February 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6gal is ~~ON HOLD~~	+	==Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10==
		+	<StructureSection load='6gal' size='340' side='right' caption='[[6gal]], [[Resolution\|resolution]] 1.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6gal]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_(strain_k12) Escherichia coli (strain k12)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GAL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GAL 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=CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC+ACID'>CXS</scene>, <scene name='pdbligand=EJ2:NI-FE+REDUCED+ACTIVE+CENTER'>EJ2</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=LI:LITHIUM+ION'>LI</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">[[6fpw\|6fpw]], [[6fpi\|6fpi]], [[6g7r\|6g7r]]</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=6gal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gal OCA], [http://pdbe.org/6gal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gal RCSB], [http://www.ebi.ac.uk/pdbsum/6gal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gal ProSAT]</span></td></tr>
		+	</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;">
		+	== Publication Abstract from PubMed ==
		+	Catalytic long-range proton transfer in [NiFe]-hydrogenases has long been associated with a highly conserved glutamate (E) situated within 4 A of the active site. Substituting for glutamine (Q) in the O2-tolerant [NiFe]-hydrogenase-1 from Escherichia coli produces a variant (E28Q) with unique properties that have been investigated using protein film electrochemistry, protein film infrared electrochemistry, and X-ray crystallography. At pH 7 and moderate potential, E28Q displays approximately 1% of the activity of the native enzyme, high enough to allow detailed infrared measurements under steady-state conditions. Atomic-level crystal structures reveal partial displacement of the amide side chain by a hydroxide ion, the occupancy of which increases with pH or under oxidizing conditions supporting formation of the superoxidized state of the unusual proximal [4Fe-3S] cluster located nearby. Under these special conditions, the essential exit pathway for at least one of the H(+) ions produced by H2 oxidation, and assumed to be blocked in the E28Q variant, is partially repaired. During steady-state H2 oxidation at neutral pH (i.e., when the barrier to H(+) exit via Q28 is almost totally closed), the catalytic cycle is dominated by the reduced states "Nia-R" and "Nia-C", even under highly oxidizing conditions. Hence, E28 is not involved in the initial activation/deprotonation of H2, but facilitates H(+) exit later in the catalytic cycle to regenerate the initial oxidized active state, assumed to be Nia-SI. Accordingly, the oxidized inactive resting state, "Ni-B", is not produced by E28Q in the presence of H2 at high potential because Nia-SI (the precursor for Ni-B) cannot accumulate. The results have important implications for understanding the catalytic mechanism of [NiFe]-hydrogenases and the control of long-range proton-coupled electron transfer in hydrogenases and other enzymes.

-	~~Authors: Carr~~, ~~S.B~~., ~~Armstrong~~, ~~F.A.~~, ~~Evans~~, R.M.	+	Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase.,Evans RM, Ash PA, Beaton SE, Brooke EJ, Vincent KA, Carr SB, Armstrong FA J Am Chem Soc. 2018 Aug 15;140(32):10208-10220. doi: 10.1021/jacs.8b04798. Epub, 2018 Aug 2. PMID:30070475<ref>PMID:30070475</ref>

-	~~Description: Structure~~ of ~~fully reduced Hydrogenase (Hyd~~-~~1) variant E28Q collected at pH 10~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Carr, S.B]]	+	<div class="pdbe-citations 6gal" style="background-color:#fffaf0;"></div>
-	[[Category: Evans, R.M]]	+	== References ==
-	[[Category: ~~Armstrong, F.A~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Armstrong, F A]]
		+	[[Category: Carr, S B]]
		+	[[Category: Evans, R M]]
		+	[[Category: Hydrogen]]
		+	[[Category: Iron sulphur cluster]]
		+	[[Category: Nife hydrogenase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Periplasm]]

OCA at 04:53, 21 February 2019

2019-02-21T04:53:59Z

←Older revision		Revision as of 04:53, 21 February 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6gal is ON HOLD ~~until Paper Publication~~	+	The entry 6gal is ON HOLD

	Authors: Carr, S.B., Armstrong, F.A., Evans, R.M.		Authors: Carr, S.B., Armstrong, F.A., Evans, R.M.

OCA at 06:51, 2 May 2018

2018-05-02T06:51:41Z

←Older revision		Revision as of 06:51, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6gal is ON HOLD	+	The entry 6gal is ON HOLD until Paper Publication

	Authors: Carr, S.B., Armstrong, F.A., Evans, R.M.		Authors: Carr, S.B., Armstrong, F.A., Evans, R.M.

OCA: Protected "6gal" [edit=sysop:move=sysop]

2018-04-18T04:33:51Z

Protected "6gal" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:33, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6gal is ON HOLD Authors: Carr, S.B., Armstrong, F.A., Evans, R.M. Description: Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collecte...

2018-04-18T04:33:49Z

New page: '''Unreleased structure''' The entry 6gal is ON HOLD Authors: Carr, S.B., Armstrong, F.A., Evans, R.M. Description: Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collecte...

New page

'''Unreleased structure'''

The entry 6gal is ON HOLD

Authors: Carr, S.B., Armstrong, F.A., Evans, R.M.

Description: Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10
[[Category: Unreleased Structures]]
[[Category: Carr, S.B]]
[[Category: Evans, R.M]]
[[Category: Armstrong, F.A]]