7d48 - Revision history

OCA at 10:52, 27 March 2024

2024-03-27T10:52:52Z

←Older revision		Revision as of 10:52, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='7d48' size='340' side='right'caption='[[7d48]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='7d48' size='340' side='right'caption='[[7d48]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7d48]] is a 1 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=7D48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D48 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d48]] is a 1 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=7D48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D48 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.15Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[7d4j\|7d4j]], [[7d4o\|7d4o]], [[7d4s\|7d4s]], [[7d4u\|7d4u]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=7d48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d48 OCA], [https://pdbe.org/7d48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d48 RCSB], [https://www.ebi.ac.uk/pdbsum/7d48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d48 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=7d48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d48 OCA], [https://pdbe.org/7d48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d48 RCSB], [https://www.ebi.ac.uk/pdbsum/7d48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d48 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 ==~~	+
-	Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed.	+

-	~~Crystal structure and functional implication of a bacterial cyclic AMP~~-AMP-GMP ~~synthetase.,Ko TP, Wang YC, Tsai CL, Yang CS, Hou MH, Chen Y Nucleic Acids Res. 2021 Apr 9. pii: 6219115. doi: 10.1093/nar/gkab165. PMID:33836064<ref>PMID:33836064</ref>~~	+	==See Also==
-		+	*[[Cyclic GMP-AMP synthase 3D synthase\|Cyclic GMP-AMP synthase 3D synthase]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe~~-~~citations 7d48" style="background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterobacter cloacae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, Y]]	+	[[Category: Chen Y]]
-	[[Category: Hou, M H]]	+	[[Category: Hou M-H]]
-	[[Category: Ko, T P]]	+	[[Category: Ko T-P]]
-	[[Category: Tsai, C L]]	+	[[Category: Tsai C-L]]
-	[[Category: Wang, Y C]]	+	[[Category: Wang Y-C]]
-	[[Category: Yang, C S]]	+	[[Category: Yang C-S]]
-	~~[[Category: Cyclic trinucleotide synthesis nucleotidyl transferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:32, 21 April 2021

2021-04-21T08:32:29Z

←Older revision		Revision as of 08:32, 21 April 2021
Line 1:		Line 1:

	==apo-form cyclic trinucleotide synthase CdnD==		==apo-form cyclic trinucleotide synthase CdnD==
-	<StructureSection load='7d48' size='340' side='right'caption='[[7d48]]' scene=''>	+	<StructureSection load='7d48' size='340' side='right'caption='[[7d48]], [[Resolution\|resolution]] 2.15Å' 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=7D48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D48 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d48]] is a 1 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=7D48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D48 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=7d48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d48 OCA], [https://pdbe.org/7d48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d48 RCSB], [https://www.ebi.ac.uk/pdbsum/7d48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d48 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=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7d4j\|7d4j]], [[7d4o\|7d4o]], [[7d4s\|7d4s]], [[7d4u\|7d4u]]</div></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=7d48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d48 OCA], [https://pdbe.org/7d48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d48 RCSB], [https://www.ebi.ac.uk/pdbsum/7d48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d48 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 ==
		+	Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed.
		+
		+	Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase.,Ko TP, Wang YC, Tsai CL, Yang CS, Hou MH, Chen Y Nucleic Acids Res. 2021 Apr 9. pii: 6219115. doi: 10.1093/nar/gkab165. PMID:33836064<ref>PMID:33836064</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7d48" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen Y]]	+	[[Category: Chen, Y]]
-	[[Category: Hou M-H]]	+	[[Category: Hou, M H]]
-	[[Category: Ko T-P]]	+	[[Category: Ko, T P]]
-	[[Category: Tsai C-L]]	+	[[Category: Tsai, C L]]
-	[[Category: Wang Y-C]]	+	[[Category: Wang, Y C]]
-	[[Category: Yang C-S]]	+	[[Category: Yang, C S]]
		+	[[Category: Cyclic trinucleotide synthesis nucleotidyl transferase]]
		+	[[Category: Transferase]]

OCA at 06:46, 17 March 2021

2021-03-17T06:46:27Z

←Older revision		Revision as of 06:46, 17 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7d48 is ~~ON HOLD until Paper Publication~~	+	==apo-form cyclic trinucleotide synthase CdnD==
-		+	<StructureSection load='7d48' size='340' side='right'caption='[[7d48]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D48 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=7d48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d48 OCA], [https://pdbe.org/7d48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d48 RCSB], [https://www.ebi.ac.uk/pdbsum/7d48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d48 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen Y]]
		+	[[Category: Hou M-H]]
		+	[[Category: Ko T-P]]
		+	[[Category: Tsai C-L]]
		+	[[Category: Wang Y-C]]
		+	[[Category: Yang C-S]]

OCA: Protected "7d48" [edit=sysop:move=sysop]

2020-11-18T07:59:23Z

Protected "7d48" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:59, 18 November 2020

OCA: New page: '''Unreleased structure''' The entry 7d48 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2020-11-18T07:59:22Z

New page: '''Unreleased structure''' The entry 7d48 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7d48 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]