6hq7 - Revision history

OCA at 07:34, 1 May 2024

OCA — Wed, 01 May 2024 07:34:56 GMT

←Older revision		Revision as of 07:34, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='6hq7' size='340' side='right'caption='[[6hq7]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='6hq7' size='340' side='right'caption='[[6hq7]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hq7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bdeba Bdeba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HQ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hq7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellovibrio_bacteriovorus_HD100 Bdellovibrio bacteriovorus HD100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HQ7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'>MG</scene~~>, ~~<scene name='pdbligand=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</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]] 2.46Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6hq2\|6hq2]], [[6hq3\|6hq3]], [[6hq4\|6hq4]], [[6hq5\|6hq5]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Bd1971 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA])~~</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=6hq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hq7 OCA], [https://pdbe.org/6hq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hq7 RCSB], [https://www.ebi.ac.uk/pdbsum/6hq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hq7 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=6hq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hq7 OCA], [~~http~~://pdbe.org/6hq7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6hq7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6hq7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6hq7 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q6MLN6_BDEBA Q6MLN6_BDEBA]
-	Bacterial usage of the cyclic dinucleotide c-di-GMP is widespread, governing the transition between motile/sessile and unicellular/multicellular behaviors. There is limited information on c-di-GMP metabolism, particularly on regulatory mechanisms governing control of EAL c-di-GMP phosphodiesterases. Herein, we provide high-resolution structures for an EAL enzyme Bd1971, from the predatory bacterium Bdellovibrio bacteriovorus, which is controlled by a second signaling nucleotide, cAMP. The full-length cAMP-bound form reveals the sensory N-terminus to be a domain-swapped variant of the cNMP/CRP family, which in the cAMP-activated state holds the C-terminal EAL enzyme in a phosphodiesterase-active conformation. Using a truncation mutant, we trap both a half-occupied and inactive apo-form of the protein, demonstrating a series of conformational changes that alter juxtaposition of the sensory domains. We show that Bd1971 interacts with several GGDEF proteins (c-di-GMP producers), but mutants of Bd1971 do not share the discrete phenotypes of GGDEF mutants, instead having an elevated level of c-di-GMP, suggesting that the role of Bd1971 is to moderate these levels, allowing "action potentials" to be generated by each GGDEF protein to effect their specific functions.	+
-		+
-	Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase.,Cadby IT, Basford SM, Nottingham R, Meek R, Lowry R, Lambert C, Tridgett M, Till R, Ahmad R, Fung R, Hobley L, Hughes WS, Moynihan PJ, Sockett RE, Lovering AL EMBO J. 2019 Jul 29:~~e100772. doi: 10.15252~~/~~embj.2018100772. PMID:31355487<ref>PMID:31355487<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6hq7" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bdeba~~]]	+	[[Category: Bdellovibrio bacteriovorus HD100]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cadby~~, I T~~]]	+	[[Category: Cadby IT]]
-	[[Category: Lovering~~, A L]]~~	+	[[Category: Lovering AL]]
-	~~[[Category: Bdellovibrio]]~~	+
-	~~[[Category: Camp]]~~	+
-	~~[[Category: Cyclic-di-gmp]]~~	+
-	~~[[Category: Eal]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 17:21, 14 August 2019

OCA — Wed, 14 Aug 2019 17:21:05 GMT

←Older revision		Revision as of 17:21, 14 August 2019
Line 3:		Line 3:
	<StructureSection load='6hq7' size='340' side='right'caption='[[6hq7]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='6hq7' size='340' side='right'caption='[[6hq7]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hq7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bdeba Bdeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HQ7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6hq2\|6hq2]], [[6hq3\|6hq3]], [[6hq4\|6hq4]], [[6hq5\|6hq5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6hq2\|6hq2]], [[6hq3\|6hq3]], [[6hq4\|6hq4]], [[6hq5\|6hq5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Bd1971 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA])</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=6hq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hq7 OCA], [http://pdbe.org/6hq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hq7 RCSB], [http://www.ebi.ac.uk/pdbsum/6hq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hq7 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=6hq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hq7 OCA], [http://pdbe.org/6hq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hq7 RCSB], [http://www.ebi.ac.uk/pdbsum/6hq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hq7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial usage of the cyclic dinucleotide c-di-GMP is widespread, governing the transition between motile/sessile and unicellular/multicellular behaviors. There is limited information on c-di-GMP metabolism, particularly on regulatory mechanisms governing control of EAL c-di-GMP phosphodiesterases. Herein, we provide high-resolution structures for an EAL enzyme Bd1971, from the predatory bacterium Bdellovibrio bacteriovorus, which is controlled by a second signaling nucleotide, cAMP. The full-length cAMP-bound form reveals the sensory N-terminus to be a domain-swapped variant of the cNMP/CRP family, which in the cAMP-activated state holds the C-terminal EAL enzyme in a phosphodiesterase-active conformation. Using a truncation mutant, we trap both a half-occupied and inactive apo-form of the protein, demonstrating a series of conformational changes that alter juxtaposition of the sensory domains. We show that Bd1971 interacts with several GGDEF proteins (c-di-GMP producers), but mutants of Bd1971 do not share the discrete phenotypes of GGDEF mutants, instead having an elevated level of c-di-GMP, suggesting that the role of Bd1971 is to moderate these levels, allowing "action potentials" to be generated by each GGDEF protein to effect their specific functions.
		+
		+	Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase.,Cadby IT, Basford SM, Nottingham R, Meek R, Lowry R, Lambert C, Tridgett M, Till R, Ahmad R, Fung R, Hobley L, Hughes WS, Moynihan PJ, Sockett RE, Lovering AL EMBO J. 2019 Jul 29:e100772. doi: 10.15252/embj.2018100772. PMID:31355487<ref>PMID:31355487</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6hq7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bdeba]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cadby, I T]]		[[Category: Cadby, I T]]

OCA at 06:16, 31 July 2019

OCA — Wed, 31 Jul 2019 06:16:17 GMT

←Older revision		Revision as of 06:16, 31 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6hq7 is ~~ON HOLD~~	+	==Structure of EAL Enzyme Bd1971 - cGMP bound form==
-		+	<StructureSection load='6hq7' size='340' side='right'caption='[[6hq7]], [[Resolution\|resolution]] 2.46Å' scene=''>
-	~~Authors~~: ~~Lovering~~, A.L., ~~Cadby~~, I.T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6hq7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HQ7 FirstGlance]. <br>
-	~~Description~~: ~~Structure of EAL Enzyme Bd1971~~ -~~cGMP bound form~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCG:CYCLIC+GUANOSINE+MONOPHOSPHATE'>PCG</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6hq2\|6hq2]], [[6hq3\|6hq3]], [[6hq4\|6hq4]], [[6hq5\|6hq5]]</td></tr>
-	[[Category: Cadby, I.T]]	+	<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=6hq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hq7 OCA], [http://pdbe.org/6hq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hq7 RCSB], [http://www.ebi.ac.uk/pdbsum/6hq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hq7 ProSAT]</span></td></tr>
-	[[Category: Lovering, A.L]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cadby, I T]]
		+	[[Category: Lovering, A L]]
		+	[[Category: Bdellovibrio]]
		+	[[Category: Camp]]
		+	[[Category: Cyclic-di-gmp]]
		+	[[Category: Eal]]
		+	[[Category: Signaling protein]]

OCA: Protected "6hq7" [edit=sysop:move=sysop]

OCA — Wed, 03 Oct 2018 06:14:33 GMT

Protected "6hq7" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:14, 3 October 2018

OCA: New page: '''Unreleased structure''' The entry 6hq7 is ON HOLD Authors: Lovering, A.L., Cadby, I.T. Description: Structure of EAL Enzyme Bd1971 -cGMP bound form [[Category: Unreleased Structures...

OCA — Wed, 03 Oct 2018 06:14:32 GMT

New page: '''Unreleased structure''' The entry 6hq7 is ON HOLD Authors: Lovering, A.L., Cadby, I.T. Description: Structure of EAL Enzyme Bd1971 -cGMP bound form [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 6hq7 is ON HOLD

Authors: Lovering, A.L., Cadby, I.T.

Description: Structure of EAL Enzyme Bd1971 -cGMP bound form
[[Category: Unreleased Structures]]
[[Category: Cadby, I.T]]
[[Category: Lovering, A.L]]