6abj - Revision history

OCA at 09:23, 22 November 2023

2023-11-22T09:23:44Z

←Older revision		Revision as of 09:23, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6abj' size='340' side='right'caption='[[6abj]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6abj' size='340' side='right'caption='[[6abj]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6abj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pseae Pseae~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wwz 3wwz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ABJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6abj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wwz 3wwz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ABJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.86Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[3wwz\|3wwz]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ldhA, PA0927 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</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=6abj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abj OCA], [https://pdbe.org/6abj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6abj RCSB], [https://www.ebi.ac.uk/pdbsum/6abj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6abj 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=6abj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abj OCA], [https://pdbe.org/6abj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6abj RCSB], [https://www.ebi.ac.uk/pdbsum/6abj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6abj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9I530_PSEAE Q9I530_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Furukawa, N]]	+	[[Category: Furukawa N]]
-	[[Category: Miyanaga, A]]	+	[[Category: Miyanaga A]]
-	[[Category: Nakajima, M]]	+	[[Category: Nakajima M]]
-	[[Category: Taguchi, H]]	+	[[Category: Taguchi H]]
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Nadh binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 11:36, 27 April 2022

2022-04-27T11:36:06Z

←Older revision		Revision as of 11:36, 27 April 2022
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	==The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa==		==The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa==
-	<StructureSection load='6abj' size='340' side='right' caption='[[6abj]], [[Resolution\|resolution]] 1.86Å' scene=''>	+	<StructureSection load='6abj' size='340' side='right'caption='[[6abj]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6abj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ABJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6abj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wwz 3wwz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ABJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wwz\|3wwz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wwz\|3wwz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ldhA, PA0927 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ldhA, PA0927 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=6abj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abj OCA], [~~http~~://pdbe.org/6abj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6abj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6abj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6abj 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=6abj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abj OCA], [https://pdbe.org/6abj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6abj RCSB], [https://www.ebi.ac.uk/pdbsum/6abj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6abj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6abj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6abj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lactate dehydrogenase 3D structures\|Lactate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pseae]]		[[Category: Pseae]]
	[[Category: Furukawa, N]]		[[Category: Furukawa, N]]

OCA at 08:37, 26 September 2018

2018-09-26T08:37:23Z

←Older revision		Revision as of 08:37, 26 September 2018
Line 3:		Line 3:
	<StructureSection load='6abj' size='340' side='right' caption='[[6abj]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6abj' size='340' side='right' caption='[[6abj]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6abj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6abj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wwz\|3wwz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wwz\|3wwz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ldhA, PA0927 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=6abj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abj OCA], [http://pdbe.org/6abj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6abj RCSB], [http://www.ebi.ac.uk/pdbsum/6abj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6abj 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=6abj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abj OCA], [http://pdbe.org/6abj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6abj RCSB], [http://www.ebi.ac.uk/pdbsum/6abj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6abj ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseae]]
	[[Category: Furukawa, N]]		[[Category: Furukawa, N]]
	[[Category: Miyanaga, A]]		[[Category: Miyanaga, A]]

OCA at 19:43, 19 September 2018

2018-09-19T19:43:35Z

←Older revision		Revision as of 19:43, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6abj is ~~ON HOLD until Paper~~ Publication	+	==The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa==
		+	<StructureSection load='6abj' size='340' side='right' caption='[[6abj]], [[Resolution\|resolution]] 1.86Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6abj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ABJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ABJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wwz\|3wwz]]</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=6abj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6abj OCA], [http://pdbe.org/6abj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6abj RCSB], [http://www.ebi.ac.uk/pdbsum/6abj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6abj ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	d-Lactate dehydrogenases (d-LDHs) from Fusobacterium nucleatum (FnLDH) and Escherichia coli (EcLDH) exhibit positive cooperativity in substrate binding, and the Pseudomonas aeruginosa enzyme (PaLDH) shows negatively cooperative substrate binding. The apo and ternary complex structures of FnLDH and PaLDH have been determined together with the apo-EcLDH structure. The three enzymes consistently form homotetrameric structures with three symmetric axes, the P-, Q-, and R-axes, unlike Lactobacillus d-LDHs, P-axis-related dimeric enzymes, although apo-FnLDH and EcLDH form asymmetric and distorted quaternary structures. The tetrameric structure allows apo-FnLDH and EcLDH to form wide intersubunit contact surfaces between the opened catalytic domains of the two Q-axis-related subunits in coordination with their asymmetric and distorted quaternary structures. These contact surfaces comprise intersubunit hydrogen bonds and hydrophobic interactions and likely prevent the domain closure motion during initial substrate binding. In contrast, apo-PaLDH possesses a highly symmetrical quaternary structure and partially closed catalytic domains that are favorable for initial substrate binding and forms virtually no intersubunit contact surface between the catalytic domains, which present their negatively charged surfaces to each other at the subunit interface. Complex FnLDH and PaLDH possess highly symmetrical quaternary structures with closed forms of the catalytic domains, which are separate from each other at the subunit interface. Structure-based mutations successfully converted the three enzymes to their dimeric forms, which exhibited no significant cooperativity in substrate binding. These observations indicate that the three enzymes undergo typical sequential allosteric transitions to exhibit their distinctive allosteric functions through the tetrameric structures.

-	~~Authors: Furukawa~~, N., Miyanaga, A., Nakajima, M., Taguchi, H.	+	Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria.,Furukawa N, Miyanaga A, Nakajima M, Taguchi H Biochemistry. 2018 Sep 18;57(37):5388-5406. doi: 10.1021/acs.biochem.8b00557., Epub 2018 Sep 7. PMID:30149697<ref>PMID:30149697</ref>

-	~~Description: The apo-structure~~ of ~~D-lactate dehydrogenase from Pseudomonas aeruginosa~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Taguchi, H]]~~	+	<div class="pdbe-citations 6abj" style="background-color:#fffaf0;"></div>
-	~~[[Category: Nakajima, M]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Furukawa, N]]		[[Category: Furukawa, N]]
	[[Category: Miyanaga, A]]		[[Category: Miyanaga, A]]
		+	[[Category: Nakajima, M]]
		+	[[Category: Taguchi, H]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Nadh binding]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA at 19:41, 9 August 2018

2018-08-09T19:41:05Z

←Older revision		Revision as of 19:41, 9 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Furukawa, N., Miyanaga, A., Nakajima, M., Taguchi, H.		Authors: Furukawa, N., Miyanaga, A., Nakajima, M., Taguchi, H.
Line 7:		Line 7:
	Description: The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa		Description: The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Furukawa, N]]
	[[Category: Taguchi, H]]		[[Category: Taguchi, H]]
	[[Category: Nakajima, M]]		[[Category: Nakajima, M]]
		+	[[Category: Furukawa, N]]
	[[Category: Miyanaga, A]]		[[Category: Miyanaga, A]]

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

2018-08-01T16:53:44Z

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

←Older revision

Revision as of 16:53, 1 August 2018

OCA: New page: '''Unreleased structure''' The entry 6abj is ON HOLD Authors: Furukawa, N., Miyanaga, A., Nakajima, M., Taguchi, H. Description: The apo-structure of D-lactate dehydrogenase from Pseud...

2018-08-01T16:53:42Z

New page: '''Unreleased structure''' The entry 6abj is ON HOLD Authors: Furukawa, N., Miyanaga, A., Nakajima, M., Taguchi, H. Description: The apo-structure of D-lactate dehydrogenase from Pseud...

New page

'''Unreleased structure'''

The entry 6abj is ON HOLD

Authors: Furukawa, N., Miyanaga, A., Nakajima, M., Taguchi, H.

Description: The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa
[[Category: Unreleased Structures]]
[[Category: Furukawa, N]]
[[Category: Taguchi, H]]
[[Category: Nakajima, M]]
[[Category: Miyanaga, A]]