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| | <StructureSection load='5j4a' size='340' side='right'caption='[[5j4a]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='5j4a' size='340' side='right'caption='[[5j4a]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5j4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pseudomallei"_whitmore_1913 "bacillus pseudomallei" whitmore 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J4A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5j4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei Burkholderia pseudomallei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J4A FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j5v|5j5v]], [[5j43|5j43]]</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]] 2.004Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cdiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913]), cdiI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913])</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=5j4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4a OCA], [https://pdbe.org/5j4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j4a RCSB], [https://www.ebi.ac.uk/pdbsum/5j4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4a ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5j4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4a OCA], [http://pdbe.org/5j4a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j4a RCSB], [http://www.ebi.ac.uk/pdbsum/5j4a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4a ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CDIA9_BURPE CDIA9_BURPE]] Toxic component of a toxin-immunity protein module, which functions as a cellular contact-dependent growth inhibition (CDI) system. CDI modules allow bacteria to communicate with and inhibit the growth of closely related neighboring bacteria in a contact-dependent fashion. The C-terminal 160 residues (CT domain) acts as a general tRNA nuclease, and inhibits growth in E.coli. Cleaves specifically within the T-loop of E.coli tRNA2(Arg). Toxic activity is neutralized by coexpression of the cognate immunity protein CdiI in E.coli, but not by non-cognate immunity proteins from other strains of B.pseudomallei.<ref>PMID:22435733</ref> | + | [https://www.uniprot.org/uniprot/CDIA9_BURPE CDIA9_BURPE] Toxic component of a toxin-immunity protein module, which functions as a cellular contact-dependent growth inhibition (CDI) system. CDI modules allow bacteria to communicate with and inhibit the growth of closely related neighboring bacteria in a contact-dependent fashion. The C-terminal 160 residues (CT domain) acts as a general tRNA nuclease, and inhibits growth in E.coli. Cleaves specifically within the T-loop of E.coli tRNA2(Arg). Toxic activity is neutralized by coexpression of the cognate immunity protein CdiI in E.coli, but not by non-cognate immunity proteins from other strains of B.pseudomallei.<ref>PMID:22435733</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: Bacillus pseudomallei whitmore 1913]] | + | [[Category: Burkholderia pseudomallei]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Goulding, C W]] | + | [[Category: Goulding CW]] |
| - | [[Category: Johnson, P M]] | + | [[Category: Johnson PM]] |
| - | [[Category: Complex]]
| + | |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Immunity protein]]
| + | |
| - | [[Category: Toxin]]
| + | |
| Structural highlights
Function
CDIA9_BURPE Toxic component of a toxin-immunity protein module, which functions as a cellular contact-dependent growth inhibition (CDI) system. CDI modules allow bacteria to communicate with and inhibit the growth of closely related neighboring bacteria in a contact-dependent fashion. The C-terminal 160 residues (CT domain) acts as a general tRNA nuclease, and inhibits growth in E.coli. Cleaves specifically within the T-loop of E.coli tRNA2(Arg). Toxic activity is neutralized by coexpression of the cognate immunity protein CdiI in E.coli, but not by non-cognate immunity proteins from other strains of B.pseudomallei.[1]
Publication Abstract from PubMed
Contact-dependent growth inhibition (CDI) is a wide-spread mechanism of inter-bacterial competition. CDI+ bacteria deploy large CdiA effector proteins, which carry variable C-terminal toxin domains (CdiA-CT). CDI+ cells also produce CdiI immunity proteins that specifically neutralize cognate CdiA-CT toxins to prevent auto-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiIE479 toxin/immunity protein complex from Burkholderia pseudomallei isolate E479. The CdiA-CTE479 tRNase domain contains a core alpha/beta-fold that is characteristic of PD-(D/E)XK superfamily nucleases. Unexpectedly, the closest structural homolog of CdiA-CTE479 is another CDI toxin domain from B. pseudomallei 1026b. Though unrelated in sequence, the two B. pseudomallei nuclease domains share similar folds and active-site architectures. By contrast, the CdiIE479 and CdiI1026b immunity proteins share no significant sequence or structural homology. CdiA-CTE479 and CdiA-CT1026b are both tRNases, however the cleavage positions are different for each nuclease. We used a molecular docking approach to model each toxin bound to tRNA substrate. The resulting models fit into electron density envelopes generated by small-angle X-ray scattering analysis of stable complexes of tRNA bound to catalytically inactive toxin domains. CdiA-CTE479 is the third CDI toxin with structural homology to the PD-(D/E)XK superfamily. PD-(D/E)XK nucleases are characterized by highly variable sequences and active-site plasticity. CDI systems exploit this structural flexibility to generate toxin diversity. These findings raise the possibility that many other uncharacterized CDI toxins may also belong to the PD-(D/E)XK superfamily.
Functional Diversity of Cytotoxic tRNase/immunity Protein Complexes from Burkholderia pseudomallei.,Johnson PM, Gucinski GC, Garza-Sanchez F, Wong T, Hung LW, Hayes CS, Goulding CW J Biol Chem. 2016 Jul 20. pii: jbc.M116.736074. PMID:27445337[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nikolakakis K, Amber S, Wilbur JS, Diner EJ, Aoki SK, Poole SJ, Tuanyok A, Keim PS, Peacock S, Hayes CS, Low DA. The toxin/immunity network of Burkholderia pseudomallei contact-dependent growth inhibition (CDI) systems. Mol Microbiol. 2012 May;84(3):516-29. doi: 10.1111/j.1365-2958.2012.08039.x. Epub, 2012 Apr 4. PMID:22435733 doi:http://dx.doi.org/10.1111/j.1365-2958.2012.08039.x
- ↑ Johnson PM, Gucinski GC, Garza-Sanchez F, Wong T, Hung LW, Hayes CS, Goulding CW. Functional Diversity of Cytotoxic tRNase/immunity Protein Complexes from Burkholderia pseudomallei. J Biol Chem. 2016 Jul 20. pii: jbc.M116.736074. PMID:27445337 doi:http://dx.doi.org/10.1074/jbc.M116.736074
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