4lj3 - Revision history

OCA at 16:20, 20 September 2023

2023-09-20T16:20:16Z

←Older revision		Revision as of 16:20, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LJ3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LJ3 FirstGlance]. <br>
-	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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]] 1.7Å</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></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=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [https://pdbe.org/4lj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [https://www.ebi.ac.uk/pdbsum/4lj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lj3 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=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [https://pdbe.org/4lj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [https://www.ebi.ac.uk/pdbsum/4lj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lj3 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:04, 14 December 2022

2022-12-14T11:04:15Z

←Older revision		Revision as of 11:04, 14 December 2022
Line 1:		Line 1:

	==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++==		==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++==
-	<StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4lj3' size='340' side='right'caption='[[4lj3]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LJ3 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>~~</td></tr>~~	+	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kie\|4kie]], [[4lyk\|4lyk]]</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=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [https://pdbe.org/4lj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [https://www.ebi.ac.uk/pdbsum/4lj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lj3 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yahA, b0315, JW0307 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [~~http~~://pdbe.org/4lj3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4lj3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4lj3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~YAHA_ECOLI YAHA_ECOLI~~]~~] Hydrolyzes~~ c-di-GMP (cyclic ~~bis~~(3'-~~5') dimeric~~ GMP) to 5'-pGpG, ~~known as PDE-A activity. PDE-B activity~~, ~~that is hydrolysis of 5'-pGpG~~ to ~~GMP, proceeds only very slowly~~.	+	[https://www.uniprot.org/uniprot/PDEL_ECOLI PDEL_ECOLI] Acts both as an enzyme and as a c-di-GMP sensor to couple transcriptional activity to the c-di-GMP status of the cell (PubMed:26553851). Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG (PubMed:15995192, PubMed:24451384, PubMed:26553851). Also acts as a transcription factor to control its own expression (PubMed:26553851).<ref>PMID:15995192</ref> <ref>PMID:24451384</ref> <ref>PMID:26553851</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Schirmer, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Sundriyal, A~~]]	+	[[Category: Schirmer T]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Sundriyal A]]
-	~~[[Category: Pgpg]]~~	+
-	~~[[Category: Phosphodiesterase]]~~	+
-	~~[[Category: Tim-barrel~~]]	+

OCA at 00:42, 5 August 2016

2016-08-05T00:42:06Z

←Older revision		Revision as of 00:42, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++==		==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++==
	<StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kie\|4kie]], [[4lyk\|4lyk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kie\|4kie]], [[4lyk\|4lyk]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yahA, b0315, JW0307 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yahA, b0315, JW0307 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lj3 PDBsum]</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=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [http://pdbe.org/4lj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lj3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4lj3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:27, 25 December 2014

2014-12-25T14:27:06Z

←Older revision		Revision as of 14:27, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. <br>	+	<table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LJ3 FirstGlance]. <br>
-	</td></tr><tr><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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene><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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kie\|4kie]], [[4lyk\|4lyk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kie\|4kie]], [[4lyk\|4lyk]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yahA, b0315, JW0307 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yahA, b0315, JW0307 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lj3 PDBsum]</span></td></tr>
-	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lj3 PDBsum]</span></td></tr>	+	</table>
-	<table>	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YAHA_ECOLI YAHA_ECOLI]] Hydrolyzes c-di-GMP (cyclic bis(3'-5') dimeric GMP) to 5'-pGpG, known as PDE-A activity. PDE-B activity, that is hydrolysis of 5'-pGpG to GMP, proceeds only very slowly.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 16:
	Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger c-di-GMP.,Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T J Biol Chem. 2014 Jan 22. PMID:24451384<ref>PMID:24451384</ref>		Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger c-di-GMP.,Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T J Biol Chem. 2014 Jan 22. PMID:24451384<ref>PMID:24451384</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase\|Phosphodiesterase]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
-	[[Category: Schirmer, T.]]	+	[[Category: Schirmer, T]]
-	[[Category: Sundriyal, A.]]	+	[[Category: Sundriyal, A]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Pgpg]]		[[Category: Pgpg]]
	[[Category: Phosphodiesterase]]		[[Category: Phosphodiesterase]]
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]

OCA at 06:54, 14 May 2014

2014-05-14T06:54:49Z

←Older revision		Revision as of 06:54, 14 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4lj3\| PDB=4lj3 \| SCENE= }}~~	+	==Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++==
-	===Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++===	+	<StructureSection load='4lj3' size='340' side='right' caption='[[4lj3]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24451384}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4lj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA]. <br>
		+	</td></tr><tr><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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HB0:TRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL'>HB0</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4kie\|4kie]], [[4lyk\|4lyk]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yahA, b0315, JW0307 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lj3 RCSB], [http://www.ebi.ac.uk/pdbsum/4lj3 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The universal second messenger cyclic di-GMP (cdG) is involved in the regulation of a diverse range of cellular processes in bacteria. The intracellular concentration of the dinucleotide is determined by the opposing actions of diguanylate cyclases (DGCs) and cdG specific phosphodiesterases (PDEs). While most PDEs have accessory domains that are involved in the regulation of their activity, the regulatory mechanism of this class of enzymes has remained unclear. Here, we use biophysical and functional analyses to show that the isolated EAL domain of a PDE from E. coli (YahA) is in a fast thermodynamic monomer - dimer equilibrium, and that the domain is active only in its dimeric state. Furthermore, our data indicate thermodynamic coupling between substrate binding and EAL dimerization with the dimerization affinity being increased about 100-fold upon substrate binding. Crystal structures of the YahA-EAL domain determined under various conditions (apo, Mg2+, c-di-GMP/Mg2+ complex) confirm structural coupling between the dimer interface and the catalytic center. The in-built regulatory properties of the EAL domain probably facilitates its modular, functional combination with the diverse repertoire of accessory domains.

-	~~==Function==~~	+	Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger c-di-GMP.,Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T J Biol Chem. 2014 Jan 22. PMID:24451384<ref>PMID:24451384</ref>
-	~~[[http://www.uniprot.org/uniprot/YAHA_ECOLI YAHA_ECOLI]] Hydrolyzes~~ c-di-GMP ~~(cyclic bis(3'-5') dimeric GMP) to 5'-pGpG~~, ~~known as PDE-~~A ~~activity. PDE-B activity~~, ~~that is hydrolysis of 5'-pGpG to GMP~~, ~~proceeds only very slowly~~.	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4lj3]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4LJ3 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024451384</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Schirmer, T.]]		[[Category: Schirmer, T.]]
	[[Category: Sundriyal, A.]]		[[Category: Sundriyal, A.]]

OCA at 03:40, 13 February 2014

2014-02-13T03:40:44Z

←Older revision		Revision as of 03:40, 13 February 2014
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	{{STRUCTURE_4lj3\| PDB=4lj3 \| SCENE= }}		{{STRUCTURE_4lj3\| PDB=4lj3 \| SCENE= }}
	===Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++===		===Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++===
		+	{{ABSTRACT_PUBMED_24451384}}

	==Function==		==Function==
Line 7:		Line 8:
	==About this Structure==		==About this Structure==
	[[4lj3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA].		[[4lj3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024451384</ref><references group="xtra"/><references/>
	[[Category: Schirmer, T.]]		[[Category: Schirmer, T.]]
	[[Category: Sundriyal, A.]]		[[Category: Sundriyal, A.]]

OCA at 07:48, 29 January 2014

2014-01-29T07:48:30Z

←Older revision		Revision as of 07:48, 29 January 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4lj3\| PDB=4lj3 \| SCENE= }}
		+	===Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++===

-	~~The entry 4lj3~~ is ~~ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/YAHA_ECOLI YAHA_ECOLI]] Hydrolyzes c-di-GMP (cyclic bis(3'-5') dimeric GMP) to 5'-pGpG, known as PDE-A activity. PDE-B activity, that is hydrolysis of 5'-pGpG to GMP, proceeds only very slowly.

-	~~Authors~~: ~~Sundriyal, A~~., Schirmer, T.	+	==About this Structure==
-		+	[[4lj3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJ3 OCA].
-	~~Description~~: ~~Crystal structure of the EAL domain of c-di~~-~~GMP specific phosphodiesterase YahA in complex with its natural substrate~~	+	[[Category: Schirmer, T.]]
		+	[[Category: Sundriyal, A.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pgpg]]
		+	[[Category: Phosphodiesterase]]
		+	[[Category: Tim-barrel]]

OCA at 06:42, 22 January 2014

2014-01-22T06:42:11Z

←Older revision		Revision as of 06:42, 22 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4lj3 is ON HOLD	+	The entry 4lj3 is ON HOLD until Paper Publication

	Authors: Sundriyal, A., Schirmer, T.		Authors: Sundriyal, A., Schirmer, T.

	Description: Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with its natural substrate		Description: Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with its natural substrate

OCA at 07:50, 21 August 2013

2013-08-21T07:50:00Z

←Older revision		Revision as of 07:50, 21 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4lj3 is ON HOLD ~~until sometime in the future~~	+	The entry 4lj3 is ON HOLD

	Authors: Sundriyal, A., Schirmer, T.		Authors: Sundriyal, A., Schirmer, T.

	Description: Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with its natural substrate		Description: Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with its natural substrate

OCA at 04:17, 1 August 2013

2013-08-01T04:17:48Z

←Older revision		Revision as of 04:17, 1 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4lj3 is ON HOLD	+	The entry 4lj3 is ON HOLD until sometime in the future

	Authors: Sundriyal, A., Schirmer, T.		Authors: Sundriyal, A., Schirmer, T.

	Description: Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with its natural substrate		Description: Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with its natural substrate