7ljl - Revision history

OCA at 14:59, 6 March 2024

2024-03-06T14:59:35Z

←Older revision		Revision as of 14:59, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='7ljl' size='340' side='right'caption='[[7ljl]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='7ljl' size='340' side='right'caption='[[7ljl]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ljl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter~~ cloacae~~" (jordan 1890) bergey et al. 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ljl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.45Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cdnD02, P853_02262 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljl OCA], [https://pdbe.org/7ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljl RCSB], [https://www.ebi.ac.uk/pdbsum/7ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljl 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=7ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljl OCA], [https://pdbe.org/7ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljl RCSB], [https://www.ebi.ac.uk/pdbsum/7ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CDND2_ENTCL CDND2_ENTCL]] CBASS (cyclic oligonucleotide-based antiphage signaling system) provides immunity against bacteriophage. The CD-NTase protein synthesizes cyclic nucleotides in response to infection; these serve as specific second messenger signals. The signals activate a diverse range of effectors, leading to bacterial cell death and thus abortive phage infection. A type II-C(AAG) CBASS system (PubMed:32839535).<ref>PMID:32544385</ref> <ref>PMID:32839535</ref> Cyclic trinucleotide synthase that catalyzes the synthesis of 3',3',3'-cyclic AMP-AMP-GMP as the major product, a second messenger for cell signal transduction.<ref>PMID:30787435</ref> Protects E.coli against phage T2 infection. When the cdnD-cap2-cap3-cap4 operon is introduced in E.coli there is a more than 10(3) decrease in the efficiency of T2 plaque formation. The operon does not protect against phage T5 and only about 10-fold against T7.<ref>PMID:32544385</ref>	+	[https://www.uniprot.org/uniprot/CDND2_ENTCL CDND2_ENTCL] CBASS (cyclic oligonucleotide-based antiphage signaling system) provides immunity against bacteriophage. The CD-NTase protein synthesizes cyclic nucleotides in response to infection; these serve as specific second messenger signals. The signals activate a diverse range of effectors, leading to bacterial cell death and thus abortive phage infection. A type II-C(AAG) CBASS system (PubMed:32839535).<ref>PMID:32544385</ref> <ref>PMID:32839535</ref> Cyclic trinucleotide synthase that catalyzes the synthesis of 3',3',3'-cyclic AMP-AMP-GMP as the major product, a second messenger for cell signal transduction.<ref>PMID:30787435</ref> Protects E.coli against phage T2 infection. When the cdnD-cap2-cap3-cap4 operon is introduced in E.coli there is a more than 10(3) decrease in the efficiency of T2 plaque formation. The operon does not protect against phage T5 and only about 10-fold against T7.<ref>PMID:32544385</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are signaling proteins that initiate antiviral immunity in animal cells and cyclic-oligonucleotide-based anti-phage signaling system (CBASS) phage defense in bacteria. Upon phage recognition, bacterial CD-NTases catalyze synthesis of cyclic-oligonucleotide signals, which activate downstream effectors and execute cell death. How CD-NTases control nucleotide selection to specifically induce defense remains poorly defined. Here, we combine structural and nucleotide-analog interference-mapping approaches to identify molecular rules controlling CD-NTase specificity. Structures of the cyclic trinucleotide synthase Enterobacter cloacae CdnD reveal coordinating nucleotide interactions and a possible role for inverted nucleobase positioning during product synthesis. We demonstrate that correct nucleotide selection in the CD-NTase donor pocket results in the formation of a thermostable-protein-nucleotide complex, and we extend our analysis to establish specific patterns governing selectivity for each of the major bacterial CD-NTase clades A-H. Our results explain CD-NTase specificity and enable predictions of nucleotide second-messenger signals within diverse antiviral systems.	+
-		+
-	Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense.,Govande AA, Duncan-Lowey B, Eaglesham JB, Whiteley AT, Kranzusch PJ Cell Rep. 2021 Jun 1;35(9):109206. doi: 10.1016/j.celrep.2021.109206. PMID:34077735<ref>PMID:34077735</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7ljl" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterobacter cloacae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Eaglesham~~, J B~~]]	+	[[Category: Eaglesham JB]]
-	[[Category: Govande, A]]	+	[[Category: Govande A]]
-	[[Category: Kranzusch~~, P J~~]]	+	[[Category: Kranzusch PJ]]
-	[[Category: Lowey, B]]	+	[[Category: Lowey B]]
-	[[Category: Whiteley~~, A W]]~~	+	[[Category: Whiteley AW]]
-	~~[[Category: Cbass]]~~	+
-	~~[[Category: Cd-ntase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trinucleotide~~]]	+

OCA at 10:10, 14 July 2021

2021-07-14T10:10:58Z

←Older revision		Revision as of 10:10, 14 July 2021
Line 1:		Line 1:

	==Structure of the Enterobacter cloacae CD-NTase CdnD in complex with ATP==		==Structure of the Enterobacter cloacae CD-NTase CdnD in complex with ATP==
-	<StructureSection load='7ljl' size='340' side='right'caption='[[7ljl]]' scene=''>	+	<StructureSection load='7ljl' size='340' side='right'caption='[[7ljl]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ljl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJL FirstGlance]. <br>
-	</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=7ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljl OCA], [https://pdbe.org/7ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljl RCSB], [https://www.ebi.ac.uk/pdbsum/7ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljl ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cdnD02, P853_02262 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</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=7ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljl OCA], [https://pdbe.org/7ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljl RCSB], [https://www.ebi.ac.uk/pdbsum/7ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CDND2_ENTCL CDND2_ENTCL]] CBASS (cyclic oligonucleotide-based antiphage signaling system) provides immunity against bacteriophage. The CD-NTase protein synthesizes cyclic nucleotides in response to infection; these serve as specific second messenger signals. The signals activate a diverse range of effectors, leading to bacterial cell death and thus abortive phage infection. A type II-C(AAG) CBASS system (PubMed:32839535).<ref>PMID:32544385</ref> <ref>PMID:32839535</ref> Cyclic trinucleotide synthase that catalyzes the synthesis of 3',3',3'-cyclic AMP-AMP-GMP as the major product, a second messenger for cell signal transduction.<ref>PMID:30787435</ref> Protects E.coli against phage T2 infection. When the cdnD-cap2-cap3-cap4 operon is introduced in E.coli there is a more than 10(3) decrease in the efficiency of T2 plaque formation. The operon does not protect against phage T5 and only about 10-fold against T7.<ref>PMID:32544385</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are signaling proteins that initiate antiviral immunity in animal cells and cyclic-oligonucleotide-based anti-phage signaling system (CBASS) phage defense in bacteria. Upon phage recognition, bacterial CD-NTases catalyze synthesis of cyclic-oligonucleotide signals, which activate downstream effectors and execute cell death. How CD-NTases control nucleotide selection to specifically induce defense remains poorly defined. Here, we combine structural and nucleotide-analog interference-mapping approaches to identify molecular rules controlling CD-NTase specificity. Structures of the cyclic trinucleotide synthase Enterobacter cloacae CdnD reveal coordinating nucleotide interactions and a possible role for inverted nucleobase positioning during product synthesis. We demonstrate that correct nucleotide selection in the CD-NTase donor pocket results in the formation of a thermostable-protein-nucleotide complex, and we extend our analysis to establish specific patterns governing selectivity for each of the major bacterial CD-NTase clades A-H. Our results explain CD-NTase specificity and enable predictions of nucleotide second-messenger signals within diverse antiviral systems.
		+
		+	Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense.,Govande AA, Duncan-Lowey B, Eaglesham JB, Whiteley AT, Kranzusch PJ Cell Rep. 2021 Jun 1;35(9):109206. doi: 10.1016/j.celrep.2021.109206. PMID:34077735<ref>PMID:34077735</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ljl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Eaglesham JB]]	+	[[Category: Eaglesham, J B]]
-	[[Category: Govande A]]	+	[[Category: Govande, A]]
-	[[Category: Kranzusch PJ]]	+	[[Category: Kranzusch, P J]]
-	[[Category: Lowey B]]	+	[[Category: Lowey, B]]
-	[[Category: Whiteley AW]]	+	[[Category: Whiteley, A W]]
		+	[[Category: Cbass]]
		+	[[Category: Cd-ntase]]
		+	[[Category: Transferase]]
		+	[[Category: Trinucleotide]]

OCA at 14:35, 2 June 2021

2021-06-02T14:35:33Z

←Older revision		Revision as of 14:35, 2 June 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7ljl is ~~ON HOLD until Paper Publication~~	+	==Structure of the Enterobacter cloacae CD-NTase CdnD in complex with ATP==
-		+	<StructureSection load='7ljl' size='340' side='right'caption='[[7ljl]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJL FirstGlance]. <br>
-	~~Description~~:	+	</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=7ljl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljl OCA], [https://pdbe.org/7ljl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljl RCSB], [https://www.ebi.ac.uk/pdbsum/7ljl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljl ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Eaglesham JB]]
		+	[[Category: Govande A]]
		+	[[Category: Kranzusch PJ]]
		+	[[Category: Lowey B]]
		+	[[Category: Whiteley AW]]

OCA at 05:38, 24 February 2021

2021-02-24T05:38:16Z

←Older revision		Revision as of 05:38, 24 February 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ljl is ON HOLD	+	The entry 7ljl is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7ljl" [edit=sysop:move=sysop]

2021-02-10T09:17:39Z

Protected "7ljl" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:17, 10 February 2021

OCA: New page: '''Unreleased structure''' The entry 7ljl is ON HOLD Authors: Description: Category: Unreleased Structures

2021-02-10T09:17:38Z

New page: '''Unreleased structure''' The entry 7ljl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ljl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]