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| | ==NMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment (AUACA)== | | ==NMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment (AUACA)== |
| - | <StructureSection load='2c06' size='340' side='right'caption='[[2c06]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='2c06' size='340' side='right'caption='[[2c06]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2c06]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C06 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2c06]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C06 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m1f|1m1f]]</div></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2c06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c06 OCA], [https://pdbe.org/2c06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c06 RCSB], [https://www.ebi.ac.uk/pdbsum/2c06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c06 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=2c06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c06 OCA], [https://pdbe.org/2c06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c06 RCSB], [https://www.ebi.ac.uk/pdbsum/2c06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c06 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/PEMK_ECOLX PEMK_ECOLX]] Toxic component of a type II toxin-antitoxin (TA) module. Probably functions as an endoribonuclease. Responsible for the stable maintenance of the plasmid during cell division by postsegregational killing of plasmid-less daughter cells. Neutralized by coexpression with cognate antitoxin PemI. Both PemI and PemK proteins bind to the promoter region of the pem operon to autoregulate their synthesis.<ref>PMID:2832364</ref> <ref>PMID:8455570</ref>
| + | [https://www.uniprot.org/uniprot/PEMK_ECOLX PEMK_ECOLX] Toxic component of a type II toxin-antitoxin (TA) module. Probably functions as an endoribonuclease. Responsible for the stable maintenance of the plasmid during cell division by postsegregational killing of plasmid-less daughter cells. Neutralized by coexpression with cognate antitoxin PemI. Both PemI and PemK proteins bind to the promoter region of the pem operon to autoregulate their synthesis.<ref>PMID:2832364</ref> <ref>PMID:8455570</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Boelens, R]] | + | [[Category: Boelens R]] |
| - | [[Category: Bonvin, A M.J J]] | + | [[Category: Bonvin AMJJ]] |
| - | [[Category: Diaz-Orejas, R]] | + | [[Category: Diaz-Orejas R]] |
| - | [[Category: Heuvel, R H.H Van Den]]
| + | [[Category: Kamphuis MB]] |
| - | [[Category: Kamphuis, M B]] | + | [[Category: Lemonnier M]] |
| - | [[Category: Lemonnier, M]] | + | [[Category: Monti MC]] |
| - | [[Category: Monti, M C]] | + | [[Category: Munoz-Gomez A]] |
| - | [[Category: Munoz-Gomez, A]] | + | [[Category: Van Den Heuvel RHH]] |
| - | [[Category: Dna replication]] | + | |
| - | [[Category: Docking]]
| + | |
| - | [[Category: Mazf]]
| + | |
| - | [[Category: Plasmid maintenance]]
| + | |
| - | [[Category: Post segregational killing]]
| + | |
| - | [[Category: Protein-rna complex]]
| + | |
| - | [[Category: Ribonuclease]]
| + | |
| - | [[Category: Rna cleavage]]
| + | |
| - | [[Category: Rnase]]
| + | |
| - | [[Category: Toxin]]
| + | |
| - | [[Category: Toxin-antitoxin]]
| + | |
| Structural highlights
Function
PEMK_ECOLX Toxic component of a type II toxin-antitoxin (TA) module. Probably functions as an endoribonuclease. Responsible for the stable maintenance of the plasmid during cell division by postsegregational killing of plasmid-less daughter cells. Neutralized by coexpression with cognate antitoxin PemI. Both PemI and PemK proteins bind to the promoter region of the pem operon to autoregulate their synthesis.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The toxin Kid and antitoxin Kis are encoded by the parD operon of Escherichia coli plasmid R1. Kid and its chromosomal homologues MazF and ChpBK have been shown to inhibit protein synthesis in cell extracts and to act as ribosome-independent endoribonucleases in vitro. Kid cleaves RNA preferentially at the 5' side of the A residue in the nucleotide sequence 5'-UA(A/C)-3' of single-stranded regions. Here, we show that RNA cleavage by Kid yields two fragments with a 2':3'-cyclic phosphate group and a free 5'-OH group, respectively. The cleavage mechanism is similar to that of RNases A and T1, involving the uracil 2'-OH group. Via NMR titration studies with an uncleavable RNA mimic, we demonstrate that residues of both monomers of the Kid dimer together form a concatenated RNA-binding surface. Docking calculations based on the NMR chemical shifts, the cleavage mechanism and previously reported mutagenesis data provide a detailed picture of the position of the AUACA fragment within the binding pocket. We propose that residues D75, R73 and H17 form the active site of the Kid toxin, where D75 and R73 are the catalytic base and acid, respectively. The RNA sequence specificity is defined by residues T46, S47, A55, F57, T69, V71 and R73. Our data show the importance of these residues for Kid function, and the implications of our results for related toxins, such as MazF, CcdB and RelE, are discussed.
Model for RNA binding and the catalytic site of the RNase Kid of the bacterial parD toxin-antitoxin system.,Kamphuis MB, Bonvin AM, Monti MC, Lemonnier M, Munoz-Gomez A, van den Heuvel RH, Diaz-Orejas R, Boelens R J Mol Biol. 2006 Mar 17;357(1):115-26. Epub 2005 Dec 27. PMID:16413033[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tsuchimoto S, Ohtsubo H, Ohtsubo E. Two genes, pemK and pemI, responsible for stable maintenance of resistance plasmid R100. J Bacteriol. 1988 Apr;170(4):1461-6. PMID:2832364
- ↑ Tsuchimoto S, Ohtsubo E. Autoregulation by cooperative binding of the PemI and PemK proteins to the promoter region of the pem operon. Mol Gen Genet. 1993 Feb;237(1-2):81-8. PMID:8455570
- ↑ Kamphuis MB, Bonvin AM, Monti MC, Lemonnier M, Munoz-Gomez A, van den Heuvel RH, Diaz-Orejas R, Boelens R. Model for RNA binding and the catalytic site of the RNase Kid of the bacterial parD toxin-antitoxin system. J Mol Biol. 2006 Mar 17;357(1):115-26. Epub 2005 Dec 27. PMID:16413033 doi:10.1016/j.jmb.2005.12.033
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