5jvl - Revision history

OCA at 19:11, 20 September 2023

OCA — Wed, 20 Sep 2023 19:11:05 GMT

←Older revision		Revision as of 19:11, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jvl' size='340' side='right'caption='[[5jvl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5jvl' size='340' side='right'caption='[[5jvl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jvl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Clustered_yellowtops Clustered yellowtops~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jvl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Flaveria_trinervia Flaveria trinervia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JVL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NQ:2-BROMO-2-DEOXYADENOSINE+5-[BETA,GAMMA-IMIDE]TRIPHOSPHORIC+ACID'>6NQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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]] 2.9Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPDK, PDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4227 Clustered yellowtops])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NQ:2-BROMO-2-DEOXYADENOSINE+5-[BETA,GAMMA-IMIDE]TRIPHOSPHORIC+ACID'>6NQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </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=5jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvl OCA], [https://pdbe.org/5jvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jvl RCSB], [https://www.ebi.ac.uk/pdbsum/5jvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvl 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=5jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvl OCA], [~~http~~://pdbe.org/5jvl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jvl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jvl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvl ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PPDK_FLATR PPDK_FLATR]] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.	+	[https://www.uniprot.org/uniprot/PPDK_FLATR PPDK_FLATR] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clustered yellowtops~~]]	+	[[Category: Flaveria trinervia]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pyruvate, phosphate dikinase]]~~	+	[[Category: Groth G]]
-	[[Category: Groth, G]]	+	[[Category: Hoeppner A]]
-	[[Category: Hoeppner, A]]	+	[[Category: Minges A]]
-	[[Category: Minges, A]]	+
-	~~[[Category: Conformational transition]]~~	+
-	~~[[Category: Nucleotide binding]]~~	+
-	~~[[Category: Phosphotransferase]]~~	+
-	~~[[Category: Swiveling mechanism]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:54, 22 April 2020

OCA — Wed, 22 Apr 2020 05:54:16 GMT

←Older revision		Revision as of 05:54, 22 April 2020
Line 1:		Line 1:

	==C4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue==		==C4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue==
-	<StructureSection load='5jvl' size='340' side='right' caption='[[5jvl]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5jvl' size='340' side='right'caption='[[5jvl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jvl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jvl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clustered_yellowtops Clustered yellowtops]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JVL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6NQ:2-BROMO-2-DEOXYADENOSINE+5-[BETA,GAMMA-IMIDE]TRIPHOSPHORIC+ACID'>6NQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NQ:2-BROMO-2-DEOXYADENOSINE+5-[BETA,GAMMA-IMIDE]TRIPHOSPHORIC+ACID'>6NQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPDK, PDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4227 Clustered yellowtops])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </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=5jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvl OCA], [http://pdbe.org/5jvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jvl RCSB], [http://www.ebi.ac.uk/pdbsum/5jvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvl 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=5jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvl OCA], [http://pdbe.org/5jvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jvl RCSB], [http://www.ebi.ac.uk/pdbsum/5jvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5jvl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jvl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyruvate phosphate dikinase\|Pyruvate phosphate dikinase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clustered yellowtops]]
		+	[[Category: Large Structures]]
	[[Category: Pyruvate, phosphate dikinase]]		[[Category: Pyruvate, phosphate dikinase]]
	[[Category: Groth, G]]		[[Category: Groth, G]]

OCA at 04:54, 12 April 2017

OCA — Wed, 12 Apr 2017 04:54:50 GMT

←Older revision		Revision as of 04:54, 12 April 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PPDK_FLATR PPDK_FLATR]] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.		[[http://www.uniprot.org/uniprot/PPDK_FLATR PPDK_FLATR]] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.
		+
		+	Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.,Minges A, Ciupka D, Winkler C, Hoppner A, Gohlke H, Groth G Sci Rep. 2017 Mar 30;7:45389. doi: 10.1038/srep45389. PMID:28358005<ref>PMID:28358005</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jvl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:26, 5 April 2017

OCA — Wed, 05 Apr 2017 13:26:40 GMT

←Older revision		Revision as of 13:26, 5 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jvl is ~~ON HOLD until Paper Publication~~	+	==C4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue==
-		+	<StructureSection load='5jvl' size='340' side='right' caption='[[5jvl]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jvl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JVL FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6NQ:2-BROMO-2-DEOXYADENOSINE+5-[BETA,GAMMA-IMIDE]TRIPHOSPHORIC+ACID'>6NQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate,_phosphate_dikinase Pyruvate, phosphate dikinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.9.1 2.7.9.1] </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=5jvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jvl OCA], [http://pdbe.org/5jvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jvl RCSB], [http://www.ebi.ac.uk/pdbsum/5jvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jvl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PPDK_FLATR PPDK_FLATR]] Formation of phosphoenolpyruvate, which is the primary acceptor of CO(2) in C4 and some Crassulacean acid metabolism plants.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pyruvate, phosphate dikinase]]
		+	[[Category: Groth, G]]
		+	[[Category: Hoeppner, A]]
		+	[[Category: Minges, A]]
		+	[[Category: Conformational transition]]
		+	[[Category: Nucleotide binding]]
		+	[[Category: Phosphotransferase]]
		+	[[Category: Swiveling mechanism]]
		+	[[Category: Transferase]]

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

OCA — Wed, 01 Jun 2016 13:54:30 GMT

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

←Older revision

Revision as of 13:54, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jvl is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 13:54:29 GMT

New page: '''Unreleased structure''' The entry 5jvl is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5jvl is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]