6p7p - Revision history

OCA at 07:24, 11 October 2023

OCA — Wed, 11 Oct 2023 07:24:29 GMT

←Older revision		Revision as of 07:24, 11 October 2023
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	<StructureSection load='6p7p' size='340' side='right'caption='[[6p7p]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='6p7p' size='340' side='right'caption='[[6p7p]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p7p]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Escherichia_coli_ms_115~~-1 Escherichia coli ms 115-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P7P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p7p]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_MS_115-1 Escherichia coli MS 115-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P7P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.665Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6p7o\|6p7o]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">HMPREF9540_01761 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=749537 Escherichia coli MS 115-1])~~</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=6p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7p OCA], [https://pdbe.org/6p7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p7p RCSB], [https://www.ebi.ac.uk/pdbsum/6p7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7p 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=6p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7p OCA], [~~http~~://pdbe.org/6p7p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p7p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p7p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7p ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NUCC_ECOM1 NUCC_ECOM1] 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 III-C(AAA) CBASS system (PubMed:32839535).<ref>PMID:31932165</ref> <ref>PMID:32839535</ref> A cyclic nucleotide-activated dsDNase. In the presence of 3',3',3'-cyclic AMP-AMP-AMP (cAAA), and to a lesser extent 3',3',3'-cyclic AMP-AMP-GMP (cAAG) and cyclic-di-AMP (c-di-AMP), endonucleolytically degrades dsDNA (PubMed:31932165, PubMed:31932164). Binds one cAAA in a pocket on one surface of the trimer; cAAA binding promotes hexamerization, which is necessary for nuclease activation. Also binds c-diAMP or linear di-AMP with lower affinity. The nuclease digests dsDNA to about 50 bp lengths with a 2-base 3' overhang and a consensus recognition site of 5'-Axx\|T-3'. DNA has been modeled to contact a pair of juxtaposed active sites (one from each layer of the hexamer), accounting for cleavage on both strands and the 2-base overhang (PubMed:31932164).<ref>PMID:31932164</ref> <ref>PMID:31932165</ref> Protects E.coli strain JP313 against bacteriophage lambda cI- infection. When the cdnC-cap7-cap6-nucC operon is transformed into a susceptible strain it confers bacteriophage immunity. Mutations in the sensor (Cap7 also called HORMA) or effector proteins (CdnC, NucC) but not the disassembly protein (Cap6 also called Trip13) no longer confer immunity. The presence of the intact operon leads to culture collapse and cell death which occurs before the phage has finished its replication cycle, thus protecting non-infected bacteria by aborting the phage infection and preventing its propagation.<ref>PMID:31932164</ref> <ref>PMID:31932165</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Escherichia coli ms 115-1]]	+	[[Category: Escherichia coli MS 115-1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berg~~, K R~~]]	+	[[Category: Berg KR]]
-	[[Category: Corbett~~, K D~~]]	+	[[Category: Corbett KD]]
-	[[Category: Lau~~, R K~~]]	+	[[Category: Lau RK]]
-	[[Category: Ye, Q]]	+	[[Category: Ye Q]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Nuclease~~]]	+

OCA at 16:16, 29 January 2020

OCA — Wed, 29 Jan 2020 16:16:00 GMT

←Older revision		Revision as of 16:16, 29 January 2020
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	<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=6p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7p OCA], [http://pdbe.org/6p7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p7p RCSB], [http://www.ebi.ac.uk/pdbsum/6p7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7p 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=6p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7p OCA], [http://pdbe.org/6p7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p7p RCSB], [http://www.ebi.ac.uk/pdbsum/6p7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteria possess an array of defenses against foreign invaders, including a broadly distributed bacteriophage defense system termed CBASS (cyclic oligonucleotide-based anti-phage signaling system). In CBASS systems, a cGAS/DncV-like nucleotidyltransferase synthesizes cyclic di- or tri-nucleotide second messengers in response to infection, and these molecules activate diverse effectors to mediate bacteriophage immunity via abortive infection. Here, we show that the CBASS effector NucC is related to restriction enzymes but uniquely assembles into a homotrimer. Binding of NucC trimers to a cyclic tri-adenylate second messenger promotes assembly of a NucC homohexamer competent for non-specific double-strand DNA cleavage. In infected cells, NucC activation leads to complete destruction of the bacterial chromosome, causing cell death prior to completion of phage replication. In addition to CBASS systems, we identify NucC homologs in over 30 type III CRISPR/Cas systems, where they likely function as accessory nucleases activated by cyclic oligoadenylate second messengers synthesized by these systems' effector complexes.
		+
		+	Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity.,Lau RK, Ye Q, Birkholz EA, Berg KR, Patel L, Mathews IT, Watrous JD, Ego K, Whiteley AT, Lowey B, Mekalanos JJ, Kranzusch PJ, Jain M, Pogliano J, Corbett KD Mol Cell. 2020 Jan 6. pii: S1097-2765(19)30923-2. doi:, 10.1016/j.molcel.2019.12.010. PMID:31932164<ref>PMID:31932164</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6p7p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:42, 22 January 2020

OCA — Wed, 22 Jan 2020 16:42:21 GMT

←Older revision		Revision as of 16:42, 22 January 2020
Line 3:		Line 3:
	<StructureSection load='6p7p' size='340' side='right'caption='[[6p7p]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='6p7p' size='340' side='right'caption='[[6p7p]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p7p]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p7p]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_ms_115-1 Escherichia coli ms 115-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P7P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p7o\|6p7o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p7o\|6p7o]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMPREF9540_01761 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=749537 Escherichia coli MS 115-1])</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=6p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7p OCA], [http://pdbe.org/6p7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p7p RCSB], [http://www.ebi.ac.uk/pdbsum/6p7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7p 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=6p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7p OCA], [http://pdbe.org/6p7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p7p RCSB], [http://www.ebi.ac.uk/pdbsum/6p7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7p ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli ms 115-1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Berg, K R]]		[[Category: Berg, K R]]

OCA at 09:09, 25 December 2019

OCA — Wed, 25 Dec 2019 09:09:59 GMT

←Older revision		Revision as of 09:09, 25 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6p7p ~~is ON HOLD until Jun 06 2021~~	+	==Structure of E. coli MS115-1 NucC, cAAA-bound form==
-		+	<StructureSection load='6p7p' size='340' side='right'caption='[[6p7p]], [[Resolution\|resolution]] 1.67Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6p7p]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P7P FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p7o\|6p7o]]</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=6p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p7p OCA], [http://pdbe.org/6p7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p7p RCSB], [http://www.ebi.ac.uk/pdbsum/6p7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p7p ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Berg, K R]]
		+	[[Category: Corbett, K D]]
		+	[[Category: Lau, R K]]
		+	[[Category: Ye, Q]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Nuclease]]

OCA at 04:15, 19 June 2019

OCA — Wed, 19 Jun 2019 04:15:10 GMT

←Older revision		Revision as of 04:15, 19 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p7p is ON HOLD	+	The entry 6p7p is ON HOLD until Jun 06 2021

	Authors:		Authors:

OCA: Protected "6p7p" [edit=sysop:move=sysop]

OCA — Wed, 12 Jun 2019 04:07:33 GMT

Protected "6p7p" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:07, 12 June 2019

OCA: New page: '''Unreleased structure''' The entry 6p7p is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 12 Jun 2019 04:07:31 GMT

New page: '''Unreleased structure''' The entry 6p7p is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6p7p is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]