6vm6: Difference between revisions

Latest revision as of 14:38, 6 March 2024

Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor with the cyclic trinucleotide 2'3'3'-cAAA

Structural highlights

6vm6 is a 11 chain structure with sequence from Acinetobacter sp. ATCC 27244 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAP4_ACIS2 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(AAAA) CBASS system (PubMed:32839535).^[1] ^[2] Binds cyclic nucleotide second messengers (synthesized by CdnD, the cognate CD-NTase in the CBASS operon). Ligand binding activates it to endonucleolytically degrade dsDNA to approximately 6 bp length fragments, with a preference for 5'-C or 5'-G cleavage site. The minor product of CdnD is the activating nucleotide; also binds the major product (2',3',3'-cyclic AMP-AMP-AMP) but is not activated by it. Only binds DNA in the presence of ligand. Is not activated by c-di-AMP, c-di-GMP, 3'3'-cyclic GMP-AMP (3'3'-cGAMP) or 3',3',3'-cyclic AMP-AMP-GMP.^[3]

References

↑ Millman A, Melamed S, Amitai G, Sorek R. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nat Microbiol. 2020 Dec;5(12):1608-1615. doi: 10.1038/s41564-020-0777-y. Epub, 2020 Aug 24. PMID:32839535 doi:https://dx.doi.org/10.1038/s41564-020-0777-y
↑ Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ. CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection. Cell. 2020 Jun 4. pii: S0092-8674(20)30614-0. doi: 10.1016/j.cell.2020.05.019. PMID:32544385 doi:https://dx.doi.org/10.1016/j.cell.2020.05.019
↑ Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ. CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection. Cell. 2020 Jun 4. pii: S0092-8674(20)30614-0. doi: 10.1016/j.cell.2020.05.019. PMID:32544385 doi:https://dx.doi.org/10.1016/j.cell.2020.05.019

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OCA

[1] Millman A, Melamed S, Amitai G, Sorek R. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nat Microbiol. 2020 Dec;5(12):1608-1615. doi: 10.1038/s41564-020-0777-y. Epub, 2020 Aug 24. PMID:32839535 doi:https://dx.doi.org/10.1038/s41564-020-0777-y

[2] Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ. CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection. Cell. 2020 Jun 4. pii: S0092-8674(20)30614-0. doi: 10.1016/j.cell.2020.05.019. PMID:32544385 doi:https://dx.doi.org/10.1016/j.cell.2020.05.019

[3] Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ. CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection. Cell. 2020 Jun 4. pii: S0092-8674(20)30614-0. doi: 10.1016/j.cell.2020.05.019. PMID:32544385 doi:https://dx.doi.org/10.1016/j.cell.2020.05.019

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6vm6 is ON HOLD
+==Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor with the cyclic trinucleotide 2'3'3'-cAAA==
+<StructureSection load='6vm6' size='340' side='right'caption='[[6vm6]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6vm6]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_sp._ATCC_27244 Acinetobacter sp. ATCC 27244] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VM6 FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6vm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vm6 OCA], [https://pdbe.org/6vm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vm6 RCSB], [https://www.ebi.ac.uk/pdbsum/6vm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vm6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAP4_ACIS2 CAP4_ACIS2] 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(AAAA) CBASS system (PubMed:32839535).<ref>PMID:32839535</ref> <ref>PMID:32544385</ref>   Binds cyclic nucleotide second messengers (synthesized by CdnD, the cognate CD-NTase in the CBASS operon). Ligand binding activates it to endonucleolytically degrade dsDNA to approximately 6 bp length fragments, with a preference for 5'-C or 5'-G cleavage site. The minor product of CdnD is the activating nucleotide; also binds the major product (2',3',3'-cyclic AMP-AMP-AMP) but is not activated by it. Only binds DNA in the presence of ligand. Is not activated by c-di-AMP, c-di-GMP, 3'3'-cyclic GMP-AMP (3'3'-cGAMP) or 3',3',3'-cyclic AMP-AMP-GMP.<ref>PMID:32544385</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Acinetobacter sp. ATCC 27244]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Antine SP]]
+[[Category: Cabrera V]]
+[[Category: Keszei AFA]]
+[[Category: Kranzusch PJ]]
+[[Category: Lee ASY]]
+[[Category: Lowey B]]
+[[Category: Mekalanos JJ]]
+[[Category: Morehouse BR]]
+[[Category: Schwede F]]
+[[Category: Shao S]]
+[[Category: Whiteley AT]]

6vm6: Difference between revisions

Latest revision as of 14:38, 6 March 2024

Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor with the cyclic trinucleotide 2'3'3'-cAAA

Structural highlights

Function

References

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