6ih7 - Revision history

OCA at 09:41, 22 November 2023

OCA — Wed, 22 Nov 2023 09:41:38 GMT

←Older revision		Revision as of 09:41, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6ih7' size='340' side='right'caption='[[6ih7]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6ih7' size='340' side='right'caption='[[6ih7]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ih7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Vibc3 Vibc3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IH7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IH7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ih7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O395 Vibrio cholerae O395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IH7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4BW:2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>4BW</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.25Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VC0395_A1247 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=345073 VIBC3])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4BW:2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>4BW</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyclic-guanylate-specific_phosphodiesterase Cyclic-guanylate-specific phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.52 3.1.4.52] </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=6ih7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ih7 OCA], [https://pdbe.org/6ih7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ih7 RCSB], [https://www.ebi.ac.uk/pdbsum/6ih7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ih7 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=6ih7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ih7 OCA], [~~http~~://pdbe.org/6ih7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ih7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ih7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ih7 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H3AJ04_VIBC3 A0A0H3AJ04_VIBC3]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cyclic-guanylate-specific phosphodiesterase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Vibc3~~]]	+	[[Category: Vibrio cholerae O395]]
-	[[Category: Pal, K]]	+	[[Category: Pal K]]
-	[[Category: Sen, U]]	+	[[Category: Sen U]]
-	[[Category: Yadav, M]]	+	[[Category: Yadav M]]
-	~~[[Category: Cyclic dinucleotide phosphodiesterase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nucleotide binding~~]]	+

OCA at 16:34, 22 January 2020

OCA — Wed, 22 Jan 2020 16:34:02 GMT

←Older revision		Revision as of 16:34, 22 January 2020
Line 3:		Line 3:
	<StructureSection load='6ih7' size='340' side='right'caption='[[6ih7]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6ih7' size='340' side='right'caption='[[6ih7]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ih7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IH7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ih7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibc3 Vibc3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IH7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4BW:2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>4BW</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4BW:2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>4BW</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VC0395_A1247 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=345073 VIBC3])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyclic-guanylate-specific_phosphodiesterase Cyclic-guanylate-specific phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.52 3.1.4.52] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyclic-guanylate-specific_phosphodiesterase Cyclic-guanylate-specific phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.52 3.1.4.52] </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=6ih7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ih7 OCA], [http://pdbe.org/6ih7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ih7 RCSB], [http://www.ebi.ac.uk/pdbsum/6ih7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ih7 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=6ih7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ih7 OCA], [http://pdbe.org/6ih7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ih7 RCSB], [http://www.ebi.ac.uk/pdbsum/6ih7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ih7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3'3'-cyclic GMP-AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5'-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5'-pGpG-Ca2+ structure, beta5-alpha5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5'-pGpG-Ca2+ structure quite different from other 5'-pGpG bound structures reported earlier.
		+
		+	Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication.,Yadav M, Pal K, Sen U Biochem J. 2019 Nov 15;476(21):3333-3353. doi: 10.1042/BCJ20190399. PMID:31647518<ref>PMID:31647518</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ih7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Cyclic-guanylate-specific phosphodiesterase]]		[[Category: Cyclic-guanylate-specific phosphodiesterase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Vibc3]]
	[[Category: Pal, K]]		[[Category: Pal, K]]
	[[Category: Sen, U]]		[[Category: Sen, U]]

OCA at 10:20, 2 October 2019

OCA — Wed, 02 Oct 2019 10:20:37 GMT

←Older revision		Revision as of 10:20, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6ih7 is ON HOLD until Paper Publication~~	+	==Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 3',3'-cGAMP bound form==
-		+	<StructureSection load='6ih7' size='340' side='right'caption='[[6ih7]], [[Resolution\|resolution]] 2.25Å' scene=''>
-	~~Authors: Yadav, M., Pal, K., Sen, U.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ih7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IH7 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 -3',3'-cGAMP bound form	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4BW:2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE'>4BW</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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/Cyclic-guanylate-specific_phosphodiesterase Cyclic-guanylate-specific phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.52 3.1.4.52] </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=6ih7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ih7 OCA], [http://pdbe.org/6ih7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ih7 RCSB], [http://www.ebi.ac.uk/pdbsum/6ih7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ih7 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cyclic-guanylate-specific phosphodiesterase]]
		+	[[Category: Large Structures]]
		+	[[Category: Pal, K]]
	[[Category: Sen, U]]		[[Category: Sen, U]]
-	[[Category: Pal, K]]
	[[Category: Yadav, M]]		[[Category: Yadav, M]]
		+	[[Category: Cyclic dinucleotide phosphodiesterase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nucleotide binding]]

OCA at 20:54, 5 June 2019

OCA — Wed, 05 Jun 2019 20:54:32 GMT

←Older revision		Revision as of 20:54, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ih7 is ON HOLD	+	The entry 6ih7 is ON HOLD until Paper Publication

	Authors: Yadav, M., Pal, K., Sen, U.		Authors: Yadav, M., Pal, K., Sen, U.

OCA: Protected "6ih7" [edit=sysop:move=sysop]

OCA — Wed, 10 Oct 2018 06:20:44 GMT

Protected "6ih7" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:20, 10 October 2018

OCA: New page: '''Unreleased structure''' The entry 6ih7 is ON HOLD Authors: Yadav, M., Pal, K., Sen, U. Description: Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395...

OCA — Wed, 10 Oct 2018 06:20:43 GMT

New page: '''Unreleased structure''' The entry 6ih7 is ON HOLD Authors: Yadav, M., Pal, K., Sen, U. Description: Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395...

New page

'''Unreleased structure'''

The entry 6ih7 is ON HOLD

Authors: Yadav, M., Pal, K., Sen, U.

Description: Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 -3',3'-cGAMP bound form
[[Category: Unreleased Structures]]
[[Category: Sen, U]]
[[Category: Pal, K]]
[[Category: Yadav, M]]