8tk0

From Proteopedia

(Difference between revisions)

Current revision

Structure of Gabija AB complex

Structural highlights

8tk0 is a 4 chain structure with sequence from Bacillus cereus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.23Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GAJA_BACC6 Component of antiviral defense system Gabija type I, composed of GajA and GajB (PubMed:29371424). Endonuclease that nicks double-stranded DNA within the sequence 5'-TNNNCGGGNNA-3' in the absence of nucleotides (NTP, dNTP and NDPs), cleaving after C-1 (PubMed:33885789, PubMed:37992757). Has no detected ATPase activity (PubMed:33885789). Expression of Gabija type I in B.subtilis (strain BEST7003) confers resistance to phages phi105, phi29, rho14, SpBeta and SBSphiC (PubMed:29371424). Expression of Gabija type I in E.coli B (strain ATCC 11303) confers resistance to phage T7 (PubMed:33885789). It is thought that this enzyme is strongly suppressed during physiological growth (in E.coli total nucleotide concentration is over 8.7 mM in mid-log phase), but during viral replication, when nucleotides are rapidly consumed, it is de-suppressed and degrades target DNA (Probable).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of Bacillus cereus GajA and GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.

Molecular basis of Gabija anti-phage supramolecular assemblies.,Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM Nat Struct Mol Biol. 2024 Aug;31(8):1243-1250. doi: 10.1038/s41594-024-01283-w. , Epub 2024 Apr 16. PMID:38627580^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R. Systematic discovery of antiphage defense systems in the microbial pangenome. Science. 2018 Mar 2;359(6379):eaar4120. PMID:29371424 doi:10.1126/science.aar4120
↑ Cheng R, Huang F, Wu H, Lu X, Yan Y, Yu B, Wang X, Zhu B. A nucleotide-sensing endonuclease from the Gabija bacterial defense system. Nucleic Acids Res. 2021 May 21;49(9):5216-5229. PMID:33885789 doi:10.1093/nar/gkab277
↑ Antine SP, Johnson AG, Mooney SE, Leavitt A, Mayer ML, Yirmiya E, Amitai G, Sorek R, Kranzusch PJ. Structural basis of Gabija anti-phage defence and viral immune evasion. Nature. 2024 Jan;625(7994):360-365. PMID:37992757 doi:10.1038/s41586-023-06855-2
↑ Cheng R, Huang F, Wu H, Lu X, Yan Y, Yu B, Wang X, Zhu B. A nucleotide-sensing endonuclease from the Gabija bacterial defense system. Nucleic Acids Res. 2021 May 21;49(9):5216-5229. PMID:33885789 doi:10.1093/nar/gkab277
↑ Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM. Molecular basis of Gabija anti-phage supramolecular assemblies. Nat Struct Mol Biol. 2024 Aug;31(8):1243-1250. PMID:38627580 doi:10.1038/s41594-024-01283-w

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8tk0"

Categories: Bacillus cereus | Large Structures | Fu TM | Shen ZF | Yang XY

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8tk0 is ON HOLD
+==Structure of Gabija AB complex==
+<StructureSection load='8tk0' size='340' side='right'caption='[[8tk0]], [[Resolution|resolution]] 3.23&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8tk0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8TK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8TK0 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.23&#8491;</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=8tk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8tk0 OCA], [https://pdbe.org/8tk0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8tk0 RCSB], [https://www.ebi.ac.uk/pdbsum/8tk0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8tk0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GAJA_BACC6 GAJA_BACC6] Component of antiviral defense system Gabija type I, composed of GajA and GajB (PubMed:29371424). Endonuclease that nicks double-stranded DNA within the sequence 5'-TNNNCGGGNNA-3' in the absence of nucleotides (NTP, dNTP and NDPs), cleaving after C-1 (PubMed:33885789, PubMed:37992757). Has no detected ATPase activity (PubMed:33885789). Expression of Gabija type I in B.subtilis (strain BEST7003) confers resistance to phages phi105, phi29, rho14, SpBeta and SBSphiC (PubMed:29371424). Expression of Gabija type I in E.coli B (strain ATCC 11303) confers resistance to phage T7 (PubMed:33885789). It is thought that this enzyme is strongly suppressed during physiological growth (in E.coli total nucleotide concentration is over 8.7 mM in mid-log phase), but during viral replication, when nucleotides are rapidly consumed, it is de-suppressed and degrades target DNA (Probable).<ref>PMID:29371424</ref> <ref>PMID:33885789</ref> <ref>PMID:37992757</ref> <ref>PMID:33885789</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of Bacillus cereus GajA and GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.
-Authors:
+Molecular basis of Gabija anti-phage supramolecular assemblies.,Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM Nat Struct Mol Biol. 2024 Aug;31(8):1243-1250. doi: 10.1038/s41594-024-01283-w. , Epub 2024 Apr 16. PMID:38627580<ref>PMID:38627580</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8tk0" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacillus cereus]]
+[[Category: Large Structures]]
+[[Category: Fu TM]]
+[[Category: Shen ZF]]
+[[Category: Yang XY]]

8tk0

From Proteopedia

Current revision

Structure of Gabija AB complex

Structural highlights

Function

Publication Abstract from PubMed

References

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