4s1c - Revision history

OCA at 12:57, 1 March 2024

2024-03-01T12:57:47Z

←Older revision		Revision as of 12:57, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4s1c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4S1C FirstGlance]. <br>		<table><tr><td colspan='2'>[[4s1c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4S1C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 2.398Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [https://pdbe.org/4s1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [https://www.ebi.ac.uk/pdbsum/4s1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4s1c 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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [https://pdbe.org/4s1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [https://www.ebi.ac.uk/pdbsum/4s1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4s1c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q8Y746_LISMO Q8Y746_LISMO]		[https://www.uniprot.org/uniprot/Q8Y746_LISMO Q8Y746_LISMO]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The nucleotide cyclic di-3',5'- adenosine monophosphate (c-di-AMP) was recently identified as an essential and widespread second messenger in bacterial signaling. Among c-di-AMP-producing bacteria, altered nucleotide levels result in several physiological defects and attenuated virulence. Thus, a detailed molecular understanding of c-di-AMP metabolism is of both fundamental and practical interest. Currently, c-di-AMP degradation is recognized solely among DHH-DHHA1 domain-containing phosphodiesterases. Using chemical proteomics, we identified the Listeria monocytogenes protein PgpH as a molecular target of c-di-AMP. Biochemical and structural studies revealed that the PgpH His-Asp (HD) domain bound c-di-AMP with high affinity and specifically hydrolyzed this nucleotide to 5'-pApA. PgpH hydrolysis activity was inhibited by ppGpp, indicating a cross-talk between c-di-AMP signaling and the stringent response. Genetic analyses supported coordinated regulation of c-di-AMP levels in and out of the host. Intriguingly, a L. monocytogenes mutant that lacks c-di-AMP phosphodiesterases exhibited elevated c-di-AMP levels, hyperinduced a host type-I IFN response, and was significantly attenuated for infection. Furthermore, PgpH homologs, which belong to the 7TMR-HD family, are widespread among hundreds of c-di-AMP synthesizing microorganisms. Thus, PgpH represents a broadly conserved class of c-di-AMP phosphodiesterase with possibly other physiological functions in this crucial signaling network.
-
-	An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence.,Huynh TN, Luo S, Pensinger D, Sauer JD, Tong L, Woodward JJ Proc Natl Acad Sci U S A. 2015 Jan 12. pii: 201416485. PMID:25583510<ref>PMID:25583510</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4s1c" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:38, 15 March 2023

2023-03-15T10:38:43Z

←Older revision		Revision as of 10:38, 15 March 2023
Line 1:		Line 1:

	==Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain==		==Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain==
-	<StructureSection load='4s1c' size='340' side='right' caption='[[4s1c]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4s1c' size='340' side='right'caption='[[4s1c]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4s1c]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lismo Lismo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S1C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4S1C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4s1c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4S1C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4s1b\|4s1b]]</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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [https://pdbe.org/4s1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [https://www.ebi.ac.uk/pdbsum/4s1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4s1c ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lmo1466, pgpH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=169963 LISMO])~~</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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [~~http~~://pdbe.org/4s1c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4s1c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4s1c ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8Y746_LISMO Q8Y746_LISMO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lismo~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Luo, S]]~~	+	[[Category: Listeria monocytogenes EGD-e]]
-	~~[[Category: Tong, L]]~~	+	[[Category: Luo S]]
-	~~[[Category: C-di~~-~~amp~~]]	+	[[Category: Tong L]]
-	[[Category: ~~Hd domain~~]]	+
-	[[Category: ~~Hydrolase]]~~	+
-	~~[[Category: Listeria monocytogene]]~~	+
-	~~[[Category: Phosphodiesterase~~]]	+

OCA at 09:13, 22 November 2017

2017-11-22T09:13:47Z

←Older revision		Revision as of 09:13, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4s1c' size='340' side='right' caption='[[4s1c]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4s1c' size='340' side='right' caption='[[4s1c]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4s1c]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4S1C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4s1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lismo Lismo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4S1C FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4s1b\|4s1b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4s1b\|4s1b]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lmo1466, pgpH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=169963 LISMO])</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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [http://pdbe.org/4s1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [http://www.ebi.ac.uk/pdbsum/4s1c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4s1c 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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [http://pdbe.org/4s1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [http://www.ebi.ac.uk/pdbsum/4s1c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4s1c ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lismo]]
	[[Category: Luo, S]]		[[Category: Luo, S]]
	[[Category: Tong, L]]		[[Category: Tong, L]]

OCA at 01:23, 19 January 2017

2017-01-19T01:23:50Z

←Older revision		Revision as of 01:23, 19 January 2017
Line 1:		Line 1:
		+
	==Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain==		==Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain==
	<StructureSection load='4s1c' size='340' side='right' caption='[[4s1c]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4s1c' size='340' side='right' caption='[[4s1c]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4s1b\|4s1b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4s1b\|4s1b]]</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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [http://www.ebi.ac.uk/pdbsum/4s1c 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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [http://pdbe.org/4s1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [http://www.ebi.ac.uk/pdbsum/4s1c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4s1c ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4s1c" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:53, 12 February 2015

2015-02-12T11:53:26Z

←Older revision		Revision as of 11:53, 12 February 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain==
		+	<StructureSection load='4s1c' size='340' side='right' caption='[[4s1c]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4s1c]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4S1C FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4s1b\|4s1b]]</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=4s1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4s1c RCSB], [http://www.ebi.ac.uk/pdbsum/4s1c PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nucleotide cyclic di-3',5'- adenosine monophosphate (c-di-AMP) was recently identified as an essential and widespread second messenger in bacterial signaling. Among c-di-AMP-producing bacteria, altered nucleotide levels result in several physiological defects and attenuated virulence. Thus, a detailed molecular understanding of c-di-AMP metabolism is of both fundamental and practical interest. Currently, c-di-AMP degradation is recognized solely among DHH-DHHA1 domain-containing phosphodiesterases. Using chemical proteomics, we identified the Listeria monocytogenes protein PgpH as a molecular target of c-di-AMP. Biochemical and structural studies revealed that the PgpH His-Asp (HD) domain bound c-di-AMP with high affinity and specifically hydrolyzed this nucleotide to 5'-pApA. PgpH hydrolysis activity was inhibited by ppGpp, indicating a cross-talk between c-di-AMP signaling and the stringent response. Genetic analyses supported coordinated regulation of c-di-AMP levels in and out of the host. Intriguingly, a L. monocytogenes mutant that lacks c-di-AMP phosphodiesterases exhibited elevated c-di-AMP levels, hyperinduced a host type-I IFN response, and was significantly attenuated for infection. Furthermore, PgpH homologs, which belong to the 7TMR-HD family, are widespread among hundreds of c-di-AMP synthesizing microorganisms. Thus, PgpH represents a broadly conserved class of c-di-AMP phosphodiesterase with possibly other physiological functions in this crucial signaling network.

-	~~The entry 4s1c is ON HOLD~~	+	An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence.,Huynh TN, Luo S, Pensinger D, Sauer JD, Tong L, Woodward JJ Proc Natl Acad Sci U S A. 2015 Jan 12. pii: 201416485. PMID:25583510<ref>PMID:25583510</ref>

-	~~Authors~~: ~~Shukun~~ Luo, ~~Liang~~ Tong	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD~~ domain	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: ~~Shukun Luo, Liang Tong~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Luo, S]]
		+	[[Category: Tong, L]]
		+	[[Category: C-di-amp]]
		+	[[Category: Hd domain]]
		+	[[Category: Hydrolase]]
		+	[[Category: Listeria monocytogene]]
		+	[[Category: Phosphodiesterase]]

OCA: Protected "4s1c" [edit=sysop:move=sysop]

2015-01-21T14:09:56Z

Protected "4s1c" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:09, 21 January 2015

OCA: New page: '''Unreleased structure''' The entry 4s1c is ON HOLD Authors: Shukun Luo, Liang Tong Description: Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain [[Category: Unr...

2015-01-21T14:09:55Z

New page: '''Unreleased structure''' The entry 4s1c is ON HOLD Authors: Shukun Luo, Liang Tong Description: Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain [[Category: Unr...

New page

'''Unreleased structure'''

The entry 4s1c is ON HOLD

Authors: Shukun Luo, Liang Tong

Description: Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain
[[Category: Unreleased Structures]]
[[Category: Shukun Luo, Liang Tong]]