5o7f - Revision history

OCA at 19:10, 29 November 2023

2023-11-29T19:10:27Z

← Older revision		Revision as of 19:10, 29 November 2023
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	==Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with GMP and Mn2+==		==Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with GMP and Mn2+==
	<StructureSection load='5o7f' size='340' side='right' caption='[[5o7f]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5o7f' size='340' side='right'caption='[[5o7f]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5o7f]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thema Thema~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O7F FirstGlance]. <br>		<table><tr><td colspan='2'>[[5o7f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O7F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.9Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5o25\|5o25]], [[5o4z\|5o4z]], [[5o58\|5o58]], [[5o1u\|5o1u]], [[5o70\|5o70]]</td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_1595 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])~~</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=5o7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7f OCA], [https://pdbe.org/5o7f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o7f RCSB], [https://www.ebi.ac.uk/pdbsum/5o7f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7f 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=5o7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7f OCA], [~~http~~://pdbe.org/5o7f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o7f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o7f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7f ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q9X1T1_THEMA Q9X1T1_THEMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5o7f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5o7f" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Thema~~]]		[[Category: Large Structures]]
	[[Category: ~~Drexler, D~~]]		[[Category: Thermotoga maritima MSB8]]
	[[Category: ~~Mueller, M~~]]		[[Category: Drexler D]]
	[[Category: ~~Witte, G~~]]		[[Category: Mueller M]]
	[[Category: ~~Hydrolase]]~~		[[Category: Witte G]]
	~~[[Category: Phosphodiesterase~~]]

OCA at 07:43, 6 December 2017

2017-12-06T07:43:53Z

← Older revision		Revision as of 07:43, 6 December 2017
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	<table><tr><td colspan='2'>[[5o7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7F FirstGlance]. <br>		<table><tr><td colspan='2'>[[5o7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5o25\|5o25]], [[5o4z\|5o4z]], [[5o58\|5o58]], [[5o1u\|5o1u]], [[5o70\|5o70]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_1595 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_1595 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=5o7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7f OCA], [http://pdbe.org/5o7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7f RCSB], [http://www.ebi.ac.uk/pdbsum/5o7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7f 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=5o7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7f OCA], [http://pdbe.org/5o7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7f RCSB], [http://www.ebi.ac.uk/pdbsum/5o7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7f ProSAT]</span></td></tr>

OCA at 10:12, 15 November 2017

2017-11-15T10:12:42Z

← Older revision		Revision as of 10:12, 15 November 2017
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	<StructureSection load='5o7f' size='340' side='right' caption='[[5o7f]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5o7f' size='340' side='right' caption='[[5o7f]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5o7f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7F FirstGlance]. <br>		<table><tr><td colspan='2'>[[5o7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_1595 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=5o7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7f OCA], [http://pdbe.org/5o7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7f RCSB], [http://www.ebi.ac.uk/pdbsum/5o7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7f 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=5o7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7f OCA], [http://pdbe.org/5o7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7f RCSB], [http://www.ebi.ac.uk/pdbsum/5o7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7f ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential second messenger c-di-AMP is achieved by modulation of the diadenylate cyclase activity as well as by specific phosphodiesterases that hydrolyze c-di-AMP in the cell. We provide here structural and biochemical data on the DHH-type phosphodiesterase TmPDE (TM1595) from Thermotoga maritima. Our analysis shows that TmPDE is preferentially degrading linear dinucleotides, such as 5'-pApA, 5'-pGpG, and 5'-pApG, compared with cyclic dinucleotide substrates. The high-resolution structural data provided here describe all steps of the PDE reaction: the ligand-free enzyme, two substrate-bound states, and three post-reaction states. We can furthermore show that Pde2 from Streptococcus pneumoniae shares both structural features and substrate specificity based on small-angle X-ray scattering data and biochemical assays.

			Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.,Drexler DJ, Muller M, Rojas-Cordova CA, Bandera AM, Witte G Structure. 2017 Oct 24. pii: S0969-2126(17)30329-5. doi:, 10.1016/j.str.2017.10.001. PMID:29107484<ref>PMID:29107484</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5o7f" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Thema]]
	[[Category: Drexler, D]]		[[Category: Drexler, D]]
	[[Category: Mueller, M]]		[[Category: Mueller, M]]

OCA at 07:14, 25 October 2017

2017-10-25T07:14:10Z

← Older revision		Revision as of 07:14, 25 October 2017
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5o7f is ~~ON HOLD until Paper Publication~~		==Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with GMP and Mn2+==
			<StructureSection load='5o7f' size='340' side='right' caption='[[5o7f]], [[Resolution\|resolution]] 1.90Å' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>[[5o7f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O7F FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<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=5o7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o7f OCA], [http://pdbe.org/5o7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o7f RCSB], [http://www.ebi.ac.uk/pdbsum/5o7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o7f ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Drexler, D]]
			[[Category: Mueller, M]]
			[[Category: Witte, G]]
			[[Category: Hydrolase]]
			[[Category: Phosphodiesterase]]

OCA: Protected "5o7f" [edit=sysop:move=sysop]

2017-09-27T12:06:48Z

Protected "5o7f" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:06, 27 September 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5o7f is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T12:06:47Z

New page: '''Unreleased structure''' The entry 5o7f is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5o7f is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]