6ioy - Revision history

OCA at 09:48, 22 November 2023

OCA — Wed, 22 Nov 2023 09:48:22 GMT

←Older revision		Revision as of 09:48, 22 November 2023
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	<StructureSection load='6ioy' size='340' side='right'caption='[[6ioy]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='6ioy' size='340' side='right'caption='[[6ioy]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ioy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Porg3 Porg3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IOY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ioy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis_ATCC_33277 Porphyromonas gingivalis ATCC 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IOY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MPD:(4S)~~-~~2-METHYL-2~~,~~4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.94Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ackA, PGN_1178 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~431947 PORG3])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Acetate_kinase Acetate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.1 2.7.2.1]~~ </~~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=6ioy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ioy OCA], [https://pdbe.org/6ioy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ioy RCSB], [https://www.ebi.ac.uk/pdbsum/6ioy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ioy 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=6ioy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ioy OCA], [~~http~~://pdbe.org/6ioy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ioy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ioy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ioy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ACKA_PORG3 ACKA_PORG3]] Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction.	+	[https://www.uniprot.org/uniprot/ACKA_PORG3 ACKA_PORG3] Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction.
	<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: Acetate kinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Porg3~~]]	+	[[Category: Porphyromonas gingivalis ATCC 33277]]
-	[[Category: Kezuka, Y]]	+	[[Category: Kezuka Y]]
-	[[Category: Nonaka, T]]	+	[[Category: Nonaka T]]
-	[[Category: Yoshida, Y]]	+	[[Category: Yoshida Y]]
-	~~[[Category: Atp]]~~	+
-	~~[[Category: Essential gene]]~~	+
-	~~[[Category: Porphyromonas gingivali]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 13:38, 10 May 2019

OCA — Fri, 10 May 2019 13:38:42 GMT

←Older revision		Revision as of 13:38, 10 May 2019
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	<StructureSection load='6ioy' size='340' side='right'caption='[[6ioy]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='6ioy' size='340' side='right'caption='[[6ioy]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ioy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IOY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ioy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Porg3 Porg3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IOY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ackA, PGN_1178 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=431947 PORG3])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetate_kinase Acetate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.1 2.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetate_kinase Acetate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.1 2.7.2.1] </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=6ioy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ioy OCA], [http://pdbe.org/6ioy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ioy RCSB], [http://www.ebi.ac.uk/pdbsum/6ioy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ioy 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=6ioy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ioy OCA], [http://pdbe.org/6ioy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ioy RCSB], [http://www.ebi.ac.uk/pdbsum/6ioy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ioy ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ACKA_PORG3 ACKA_PORG3]] Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction.		[[http://www.uniprot.org/uniprot/ACKA_PORG3 ACKA_PORG3]] Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Acetyl phosphate (AcP) is generally produced from acetyl coenzyme A by phosphotransacetylase (Pta), and subsequent reaction with ADP, catalyzed by acetate kinase (Ack), produces ATP. The mechanism of ATP production in Porphyromonas gingivalis is poorly understood. The aim of this study was to explore the molecular basis of the Pta-Ack pathway in this microorganism. Pta and Ack from P. gingivalis ATCC 33277 were enzymatically and structurally characterized. Structural and mutational analyses suggest that Pta is a dimer with two substrate-binding sites in each subunit. Ack is also dimeric, with a catalytic cleft in each subunit, and structural analysis indicates a dramatic domain motion that opens and closes the cleft during catalysis. ATP formation by Ack proceeds via a sequential mechanism. Reverse transcription-PCR analysis demonstrated that the pta (PGN_1179) and ack (PGN_1178) genes, tandemly located in the genome, are cotranscribed as an operon. Inactivation of pta or ack in P. gingivalis by homologous recombination was successful only when the inactivated gene was expressed in trans. Therefore, both pta and ack genes are essential for this microorganism. Insights into the Pta-Ack pathway reported herein would be helpful to understand the energy acquisition in P. gingivalis.
		+
		+	Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production in Porphyromonas gingivalis.,Yoshida Y, Sato M, Nonaka T, Hasegawa Y, Kezuka Y J Oral Microbiol. 2019 Apr 4;11(1):1588086. doi: 10.1080/20002297.2019.1588086., eCollection 2019. PMID:31007866<ref>PMID:31007866</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ioy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Acetate kinase]]		[[Category: Acetate kinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Porg3]]
	[[Category: Kezuka, Y]]		[[Category: Kezuka, Y]]
	[[Category: Nonaka, T]]		[[Category: Nonaka, T]]

OCA at 06:51, 24 April 2019

OCA — Wed, 24 Apr 2019 06:51:32 GMT

←Older revision		Revision as of 06:51, 24 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ioy is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Porphyromonas gingivalis acetate kinase==
-		+	<StructureSection load='6ioy' size='340' side='right'caption='[[6ioy]], [[Resolution\|resolution]] 1.94Å' scene=''>
-	~~Authors~~: ~~Kezuka~~, Y., ~~Yoshida~~, Y., ~~Nonaka~~, T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ioy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IOY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IOY FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~Porphyromonas gingivalis~~ acetate kinase	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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/Acetate_kinase Acetate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.1 2.7.2.1] </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=6ioy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ioy OCA], [http://pdbe.org/6ioy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ioy RCSB], [http://www.ebi.ac.uk/pdbsum/6ioy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ioy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ACKA_PORG3 ACKA_PORG3]] Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Acetate kinase]]
		+	[[Category: Large Structures]]
		+	[[Category: Kezuka, Y]]
	[[Category: Nonaka, T]]		[[Category: Nonaka, T]]
-	[[Category: Kezuka, Y]]
	[[Category: Yoshida, Y]]		[[Category: Yoshida, Y]]
		+	[[Category: Atp]]
		+	[[Category: Essential gene]]
		+	[[Category: Porphyromonas gingivali]]
		+	[[Category: Transferase]]

OCA at 18:51, 2 December 2018

OCA — Sun, 02 Dec 2018 18:51:14 GMT

←Older revision		Revision as of 18:51, 2 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kezuka, Y., Yoshida, Y., Nonaka, T.		Authors: Kezuka, Y., Yoshida, Y., Nonaka, T.
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	Description: Crystal structure of Porphyromonas gingivalis acetate kinase		Description: Crystal structure of Porphyromonas gingivalis acetate kinase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Nonaka, T]]
	[[Category: Kezuka, Y]]		[[Category: Kezuka, Y]]
	[[Category: Yoshida, Y]]		[[Category: Yoshida, Y]]
-	[[Category: Nonaka, T]]

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

OCA — Wed, 07 Nov 2018 10:45:41 GMT

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

←Older revision

Revision as of 10:45, 7 November 2018

OCA: New page: '''Unreleased structure''' The entry 6ioy is ON HOLD Authors: Kezuka, Y., Yoshida, Y., Nonaka, T. Description: Crystal structure of Porphyromonas gingivalis acetate kinase [[Category: ...

OCA — Wed, 07 Nov 2018 10:45:40 GMT

New page: '''Unreleased structure''' The entry 6ioy is ON HOLD Authors: Kezuka, Y., Yoshida, Y., Nonaka, T. Description: Crystal structure of Porphyromonas gingivalis acetate kinase [[Category: ...

New page

'''Unreleased structure'''

The entry 6ioy is ON HOLD

Authors: Kezuka, Y., Yoshida, Y., Nonaka, T.

Description: Crystal structure of Porphyromonas gingivalis acetate kinase
[[Category: Unreleased Structures]]
[[Category: Kezuka, Y]]
[[Category: Yoshida, Y]]
[[Category: Nonaka, T]]