5kmq - Revision history

OCA at 09:14, 25 October 2023

OCA — Wed, 25 Oct 2023 09:14:23 GMT

←Older revision		Revision as of 09:14, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kmq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldalkalibacillus_thermarum_TA2.A1 Caldalkalibacillus thermarum TA2.A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KMQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kmq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldalkalibacillus_thermarum_TA2.A1 Caldalkalibacillus thermarum TA2.A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KMQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 2.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=5kmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kmq OCA], [https://pdbe.org/5kmq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kmq RCSB], [https://www.ebi.ac.uk/pdbsum/5kmq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kmq 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=5kmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kmq OCA], [https://pdbe.org/5kmq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kmq RCSB], [https://www.ebi.ac.uk/pdbsum/5kmq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kmq ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:57, 29 March 2023

OCA — Wed, 29 Mar 2023 06:57:06 GMT

←Older revision		Revision as of 06:57, 29 March 2023
Line 3:		Line 3:
	<StructureSection load='5kmq' size='340' side='right'caption='[[5kmq]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5kmq' size='340' side='right'caption='[[5kmq]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kmq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caltt Caltt~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KMQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kmq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldalkalibacillus_thermarum_TA2.A1 Caldalkalibacillus thermarum TA2.A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KMQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]], [[5kmp\|5kmp]], [[5kmr\|5kmr]], [[5kms\|5kms]]</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=5kmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kmq OCA], [https://pdbe.org/5kmq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kmq RCSB], [https://www.ebi.ac.uk/pdbsum/5kmq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kmq ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CathTA2_0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=986075 CALTT])</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=5kmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kmq OCA], [~~http~~://pdbe.org/5kmq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kmq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kmq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kmq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F5L3B8_CALTT F5L3B8_CALTT]
	<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: ~~Caltt~~]]	+	[[Category: Caldalkalibacillus thermarum TA2 A1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aragao, D]]	+	[[Category: Aragao D]]
-	[[Category: Cook~~, G M~~]]	+	[[Category: Cook GM]]
-	[[Category: Nakatani, Y]]	+	[[Category: Nakatani Y]]
-	~~[[Category: I379e mutation]]~~	+
-	~~[[Category: Nadh dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 15:29, 8 July 2020

OCA — Wed, 08 Jul 2020 15:29:14 GMT

←Older revision		Revision as of 15:29, 8 July 2020
Line 1:		Line 1:

	==The structure of I379E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum==		==The structure of I379E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum==
-	<StructureSection load='5kmq' size='340' side='right' caption='[[5kmq]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5kmq' size='340' side='right'caption='[[5kmq]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kmq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KMQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kmq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caltt Caltt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KMQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]], [[5kmp\|5kmp]], [[5kmr\|5kmr]], [[5kms\|5kms]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]], [[5kmp\|5kmp]], [[5kmr\|5kmr]], [[5kms\|5kms]]</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=5kmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kmq OCA], [http://pdbe.org/5kmq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kmq RCSB], [http://www.ebi.ac.uk/pdbsum/5kmq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kmq ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CathTA2_0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=986075 CALTT])</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=5kmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kmq OCA], [http://pdbe.org/5kmq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kmq RCSB], [http://www.ebi.ac.uk/pdbsum/5kmq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kmq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caltt]]
		+	[[Category: Large Structures]]
	[[Category: Aragao, D]]		[[Category: Aragao, D]]
	[[Category: Cook, G M]]		[[Category: Cook, G M]]

OCA at 23:24, 25 January 2017

OCA — Wed, 25 Jan 2017 23:24:32 GMT

←Older revision		Revision as of 23:24, 25 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5kmq is ~~ON HOLD until Paper~~ Publication	+	==The structure of I379E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum==
		+	<StructureSection load='5kmq' size='340' side='right' caption='[[5kmq]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kmq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KMQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KMQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nwz\|4nwz]], [[5kmp\|5kmp]], [[5kmr\|5kmr]], [[5kms\|5kms]]</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=5kmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kmq OCA], [http://pdbe.org/5kmq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kmq RCSB], [http://www.ebi.ac.uk/pdbsum/5kmq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kmq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies.

-	~~Authors~~: ~~Cook, G.M~~., ~~Aragao~~, D., ~~Nakatani~~, Y.	+	The mechanism of catalysis by type-II NADH:quinone oxidoreductases.,Blaza JN, Bridges HR, Aragao D, Dunn EA, Heikal A, Cook GM, Nakatani Y, Hirst J Sci Rep. 2017 Jan 9;7:40165. doi: 10.1038/srep40165. PMID:28067272<ref>PMID:28067272</ref>

-	~~Description: The structure~~ of ~~I379E variant~~ of ~~type II NADH dehydrogenase from Caldalkalibacillus thermarum~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5kmq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Aragao, D]]		[[Category: Aragao, D]]
		+	[[Category: Cook, G M]]
	[[Category: Nakatani, Y]]		[[Category: Nakatani, Y]]
-	[[Category: ~~Cook, G.M~~]]	+	[[Category: I379e mutation]]
		+	[[Category: Nadh dehydrogenase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA at 13:33, 10 August 2016

OCA — Wed, 10 Aug 2016 13:33:20 GMT

←Older revision		Revision as of 13:33, 10 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Cook, G.M., Aragao, D., Nakatani, Y.		Authors: Cook, G.M., Aragao, D., Nakatani, Y.

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

OCA — Wed, 13 Jul 2016 00:34:31 GMT

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

←Older revision

Revision as of 00:34, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kmq is ON HOLD Authors: Cook, G.M., Aragao, D., Nakatani, Y. Description: The structure of I379E variant of type II NADH dehydrogenase from Caldal...

OCA — Wed, 13 Jul 2016 00:34:29 GMT

New page: '''Unreleased structure''' The entry 5kmq is ON HOLD Authors: Cook, G.M., Aragao, D., Nakatani, Y. Description: The structure of I379E variant of type II NADH dehydrogenase from Caldal...

New page

'''Unreleased structure'''

The entry 5kmq is ON HOLD

Authors: Cook, G.M., Aragao, D., Nakatani, Y.

Description: The structure of I379E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum
[[Category: Unreleased Structures]]
[[Category: Aragao, D]]
[[Category: Nakatani, Y]]
[[Category: Cook, G.M]]