6pi8 - Revision history

OCA at 07:29, 11 October 2023

2023-10-11T07:29:58Z

←Older revision		Revision as of 07:29, 11 October 2023
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	<StructureSection load='6pi8' size='340' side='right'caption='[[6pi8]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='6pi8' size='340' side='right'caption='[[6pi8]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pi8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"marinobacter_subterrani"_bonis_and_gralnick_2015 "marinobacter~~ subterrani~~" bonis and gralnick 2015~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PI8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PI8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pi8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Marinobacter_subterrani Marinobacter subterrani]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PI8 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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.635Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Msub_13096 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1658765 "Marinobacter subterrani" Bonis and Gralnick 2015])</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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6pi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pi8 OCA], [~~http~~://pdbe.org/6pi8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pi8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pi8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pi8 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=6pi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pi8 OCA], [https://pdbe.org/6pi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pi8 RCSB], [https://www.ebi.ac.uk/pdbsum/6pi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pi8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0J7JFD7_9GAMM A0A0J7JFD7_9GAMM]
	<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: Marinobacter subterrani bonis and gralnick 2015]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Christianson, D W~~]]	+	[[Category: Marinobacter subterrani]]
-	[[Category: ~~Osko, J D~~]]	+	[[Category: Christianson DW]]
-	[[Category: ~~Acetylpolyamine amidohydrolase]]~~	+	[[Category: Osko JD]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase inhibitor]]~~	+
-	~~[[Category: Hydrolase-inhibitor complex]]~~	+
-	~~[[Category: Polyamine deacetylase~~]]	+

OCA at 12:26, 18 December 2019

2019-12-18T12:26:47Z

←Older revision		Revision as of 12:26, 18 December 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6pi8 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with acetate==
		+	<StructureSection load='6pi8' size='340' side='right'caption='[[6pi8]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6pi8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"marinobacter_subterrani"_bonis_and_gralnick_2015 "marinobacter subterrani" bonis and gralnick 2015]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PI8 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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Msub_13096 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1658765 "Marinobacter subterrani" Bonis and Gralnick 2015])</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=6pi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pi8 OCA], [http://pdbe.org/6pi8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pi8 RCSB], [http://www.ebi.ac.uk/pdbsum/6pi8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pi8 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polyamines are small organic cations that are essential for cellular function in all kingdoms of life. Polyamine metabolism is regulated by enzyme-catalyzed acetylation-deacetylation cycles in a fashion similar to the epigenetic regulation of histone function in eukaryotes. Bacterial polyamine deacetylases are particularly intriguing, because these enzymes share the fold and function of eukaryotic histone deacetylases. Recently, acetylpolyamine amidohydrolase from the deep earth halophile Marinobacter subterrani (msAPAH) was described. This Zn(2+)-dependent deacetylase shares 53% amino acid sequence identity with the acetylpolyamine amidohydrolase from Mycoplana ramosa (mrAPAH) and 22% amino acid sequence identity with the catalytic domain of histone deacetylase 10 from Danio rerio (zebrafish; zHDAC10), the eukaryotic polyamine deacetylase. The X-ray crystal structure of msAPAH, determined in complexes with seven different inhibitors as well as the acetate coproduct, shows how the chemical strategy of Zn(2+)-dependent amide hydrolysis and the catalytic specificity for cationic polyamine substrates is conserved in a subterranean halophile. Structural comparisons with mrAPAH reveal that an array of aspartate and glutamate residues unique to msAPAH enable the binding of one or more Mg(2+) ions in the active site and elsewhere on the protein surface. Notwithstanding these differences, activity assays with a panel of acetylpolyamine and acetyllysine substrates confirm that msAPAH is a broad-specificity polyamine deacetylase, much like mrAPAH. The broad substrate specificity contrasts with the narrow substrate specificity of zHDAC10, which is highly specific for N(8)-acetylspermidine hydrolysis. Notably, quaternary structural features govern the substrate specificity of msAPAH and mrAPAH, whereas tertiary structural features govern the substrate specificity of zHDAC10.

-	~~Authors~~:	+	Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth Halophile Marinobacter subterrani.,Osko JD, Roose BW, Shinsky SA, Christianson DW Biochemistry. 2019 Sep 10;58(36):3755-3766. doi: 10.1021/acs.biochem.9b00582., Epub 2019 Aug 27. PMID:31436969<ref>PMID:31436969</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6pi8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Marinobacter subterrani bonis and gralnick 2015]]
		+	[[Category: Large Structures]]
		+	[[Category: Christianson, D W]]
		+	[[Category: Osko, J D]]
		+	[[Category: Acetylpolyamine amidohydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase inhibitor]]
		+	[[Category: Hydrolase-inhibitor complex]]
		+	[[Category: Polyamine deacetylase]]

OCA at 04:07, 10 July 2019

2019-07-10T04:07:47Z

←Older revision		Revision as of 04:07, 10 July 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pi8 is ON HOLD	+	The entry 6pi8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6pi8" [edit=sysop:move=sysop]

2019-07-03T04:23:18Z

Protected "6pi8" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:23, 3 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pi8 is ON HOLD Authors: Description: Category: Unreleased Structures

2019-07-03T04:23:17Z

New page: '''Unreleased structure''' The entry 6pi8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pi8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]