5mf5 - Revision history

OCA at 18:41, 1 November 2023

OCA — Wed, 01 Nov 2023 18:41:42 GMT

←Older revision		Revision as of 18:41, 1 November 2023
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	<StructureSection load='5mf5' size='340' side='right'caption='[[5mf5]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='5mf5' size='340' side='right'caption='[[5mf5]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mf5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4y9q 4y9q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MF5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MF5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mf5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4y9q 4y9q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MF5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.77Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y9o\|4y9o]], [[4y9m\|4y9m]], [[4y9n\|4y9n]], [[4y9p\|4y9p]], [[4y8e\|4y8e]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AO964_02925 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5mf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mf5 OCA], [https://pdbe.org/5mf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mf5 RCSB], [https://www.ebi.ac.uk/pdbsum/5mf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mf5 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=5mf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mf5 OCA], [~~http~~://pdbe.org/5mf5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mf5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mf5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mf5 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9HXH7_PSEAE Q9HXH7_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bellini, D]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: Horrell, S]]	+	[[Category: Bellini D]]
-	[[Category: Strange, R]]	+	[[Category: Horrell S]]
-	[[Category: Wagner, A]]	+	[[Category: Strange R]]
-	[[Category: Walsh, M]]	+	[[Category: Wagner A]]
-	~~[[Category: Biofilm formation]]~~	+	[[Category: Walsh M]]
-	~~[[Category: Eal]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: P aeruginosa]]~~	+
-	~~[[Category: Pa3825]]~~	+
-	~~[[Category: Phosphodiesterase~~]]	+

OCA at 06:25, 3 July 2019

OCA — Wed, 03 Jul 2019 06:25:21 GMT

←Older revision		Revision as of 06:25, 3 July 2019
Line 1:		Line 1:

	==PA3825-EAL Mg-CdG Structure==		==PA3825-EAL Mg-CdG Structure==
-	<StructureSection load='5mf5' size='340' side='right' caption='[[5mf5]], [[Resolution\|resolution]] 1.77Å' scene=''>	+	<StructureSection load='5mf5' size='340' side='right'caption='[[5mf5]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mf5]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4y9q 4y9q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MF5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mf5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4y9q 4y9q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MF5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y9o\|4y9o]], [[4y9m\|4y9m]], [[4y9n\|4y9n]], [[4y9p\|4y9p]], [[4y8e\|4y8e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y9o\|4y9o]], [[4y9m\|4y9m]], [[4y9n\|4y9n]], [[4y9p\|4y9p]], [[4y8e\|4y8e]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AO964_02925 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5mf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mf5 OCA], [http://pdbe.org/5mf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mf5 RCSB], [http://www.ebi.ac.uk/pdbsum/5mf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mf5 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=5mf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mf5 OCA], [http://pdbe.org/5mf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mf5 RCSB], [http://www.ebi.ac.uk/pdbsum/5mf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mf5 ProSAT]</span></td></tr>
	</table>		</table>
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5mf5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mf5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase\|Phosphodiesterase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bellini, D]]		[[Category: Bellini, D]]
	[[Category: Horrell, S]]		[[Category: Horrell, S]]

OCA at 08:17, 9 March 2017

OCA — Thu, 09 Mar 2017 08:17:42 GMT

←Older revision		Revision as of 08:17, 9 March 2017
Line 8:		Line 8:
	<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=5mf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mf5 OCA], [http://pdbe.org/5mf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mf5 RCSB], [http://www.ebi.ac.uk/pdbsum/5mf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mf5 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=5mf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mf5 OCA], [http://pdbe.org/5mf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mf5 RCSB], [http://www.ebi.ac.uk/pdbsum/5mf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mf5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The bacterial second messenger cyclic di-3',5'-guanosine monophosphate (c-di-GMP) is a key regulator of bacterial motility and virulence. As high levels of c-di-GMP are associated with the biofilm lifestyle, c-di-GMP hydrolysing phosphodiesterases (PDEs) have been identified as key targets to aid development of novel strategies to treat chronic infection by exploiting biofilm dispersal. We have studied the EAL signature motif-containing phosphodiesterase domains from the Pseudomonas aeruginosa proteins PA3825 (PA3825EAL) and PA1727 (MucREAL). Different dimerisation interfaces allow us to identify interface independent principles of enzyme regulation. Unlike previously characterised two-metal binding EAL-phosphodiesterases, PA3825EAL in complex with pGpG provides a model for a third metal site. The third metal is positioned to stabilise the negative charge of the 5'-phosphate, and thus three metals could be required for catalysis in analogy to other nucleases. This newly uncovered variation in metal coordination may provide a further level of bacterial PDE regulation.
		+
		+	Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases.,Bellini D, Horrell S, Hutchin A, Phippen CW, Strange RW, Cai Y, Wagner A, Webb JS, Tews I, Walsh MA Sci Rep. 2017 Feb 10;7:42166. doi: 10.1038/srep42166. PMID:28186120<ref>PMID:28186120</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5mf5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:22, 22 December 2016

OCA — Thu, 22 Dec 2016 21:22:14 GMT

←Older revision		Revision as of 21:22, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mf5 is ~~ON HOLD~~	+	==PA3825-EAL Mg-CdG Structure==
-		+	<StructureSection load='5mf5' size='340' side='right' caption='[[5mf5]], [[Resolution\|resolution]] 1.77Å' scene=''>
-	~~Authors~~: ~~Horrell~~, S., ~~Bellini~~, D., ~~Strange~~, R., ~~Wagner~~, A., ~~Walsh, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5mf5]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4y9q 4y9q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MF5 FirstGlance]. <br>
-	~~Description~~: ~~PA3825-EAL Mg-CdG Structure~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y9o\|4y9o]], [[4y9m\|4y9m]], [[4y9n\|4y9n]], [[4y9p\|4y9p]], [[4y8e\|4y8e]]</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=5mf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mf5 OCA], [http://pdbe.org/5mf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mf5 RCSB], [http://www.ebi.ac.uk/pdbsum/5mf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mf5 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bellini, D]]
		+	[[Category: Horrell, S]]
		+	[[Category: Strange, R]]
	[[Category: Wagner, A]]		[[Category: Wagner, A]]
	[[Category: Walsh, M]]		[[Category: Walsh, M]]
-	[[Category: ~~Bellini, D~~]]	+	[[Category: Biofilm formation]]
-	[[Category: ~~Strange, R~~]]	+	[[Category: Eal]]
-	[[Category: ~~Horrell, S~~]]	+	[[Category: Hydrolase]]
		+	[[Category: P aeruginosa]]
		+	[[Category: Pa3825]]
		+	[[Category: Phosphodiesterase]]

OCA: Protected "5mf5" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 16:45:57 GMT

Protected "5mf5" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:45, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mf5 is ON HOLD Authors: Horrell, S., Bellini, D., Strange, R., Wagner, A., Walsh, M. Description: PA3825-EAL Mg-CdG Structure [[Category: Unreleas...

OCA — Fri, 09 Dec 2016 16:45:56 GMT

New page: '''Unreleased structure''' The entry 5mf5 is ON HOLD Authors: Horrell, S., Bellini, D., Strange, R., Wagner, A., Walsh, M. Description: PA3825-EAL Mg-CdG Structure [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5mf5 is ON HOLD

Authors: Horrell, S., Bellini, D., Strange, R., Wagner, A., Walsh, M.

Description: PA3825-EAL Mg-CdG Structure
[[Category: Unreleased Structures]]
[[Category: Wagner, A]]
[[Category: Walsh, M]]
[[Category: Bellini, D]]
[[Category: Strange, R]]
[[Category: Horrell, S]]