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| - | {{Seed}} | |
| - | [[Image:3m8f.png|left|200px]] | |
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| - | <!-- | + | ==Protein structure of type III plasmid segregation TubR mutant== |
| - | The line below this paragraph, containing "STRUCTURE_3m8f", creates the "Structure Box" on the page.
| + | <StructureSection load='3m8f' size='340' side='right'caption='[[3m8f]], [[Resolution|resolution]] 2.80Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[3m8f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thuringiensis_serovar_israelensis Bacillus thuringiensis serovar israelensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M8F FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</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=3m8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m8f OCA], [https://pdbe.org/3m8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m8f RCSB], [https://www.ebi.ac.uk/pdbsum/3m8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m8f ProSAT]</span></td></tr> |
| - | {{STRUCTURE_3m8f| PDB=3m8f | SCENE= }}
| + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/TUBR_BACTI TUBR_BACTI] A DNA-binding protein that is part of the type III plasmid partition system used to ensure correct segregation of the pBtoxis plasmid. Cooperatively binds to the centromere-like site (tubC), which may seed filament formation by the TubZ polymerizing GTPase, stabilizing TubZ filaments. TubR-tubC complexes track the depolymerizing minus end of the filament, probably pulling plasmid within the cell (PubMed:20534443, PubMed:23010931, PubMed:25825718). Required for plasmid replication (PubMed:16936050, PubMed:17873046). Negatively regulates levels of TubZ; its effect on RNA expression has not been shown (Probable). Specifically binds iterons, 12-bp imperfect direct repeats that function as a plasmid origin of replication (PubMed:17873046, PubMed:23010931, PubMed:25825718). Four TubR dimers bind to tubC, forming an extended bent DNA-protein filament with protein wrapping helically around the outside of the DNA (PubMed:20534443, PubMed:23010931).<ref>PMID:16936050</ref> <ref>PMID:17873046</ref> <ref>PMID:20534443</ref> <ref>PMID:23010931</ref> <ref>PMID:25825718</ref> <ref>PMID:17510284</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The segregation of plasmid DNA typically requires three elements: a DNA centromere site, an NTPase, and a centromere-binding protein. Because of their simplicity, plasmid partition systems represent tractable models to study the molecular basis of DNA segregation. Unlike eukaryotes, which utilize the GTPase tubulin to segregate DNA, the most common plasmid-encoded NTPases contain Walker-box and actin-like folds. Recently, a plasmid stability cassette on Bacillus thuringiensis pBtoxis encoding a putative FtsZ/tubulin-like NTPase called TubZ and DNA-binding protein called TubR has been described. How these proteins collaborate to impart plasmid stability, however, is unknown. Here we show that the TubR structure consists of an intertwined dimer with a winged helix-turn-helix (HTH) motif. Strikingly, however, the TubR recognition helices mediate dimerization, making canonical HTH-DNA interactions impossible. Mutagenesis data indicate that a basic patch, encompassing the two wing regions and the N termini of the recognition helices, mediates DNA binding, which indicates an unusual HTH-DNA interaction mode in which the N termini of the recognition helices insert into a single DNA groove and the wings into adjacent DNA grooves. The TubZ structure shows that it is as similar structurally to eukaryotic tubulin as it is to bacterial FtsZ. TubZ forms polymers with guanine nucleotide-binding characteristics and polymer dynamics similar to tubulin. Finally, we show that the exposed TubZ C-terminal region interacts with TubR-DNA, linking the TubR-bound pBtoxis to TubZ polymerization. The combined data suggest a mechanism for TubZ-polymer powered plasmid movement. |
| | | | |
| - | ===Protein structure of type III plasmid segregation TubR mutant===
| + | Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition.,Ni L, Xu W, Kumaraswami M, Schumacher MA Proc Natl Acad Sci U S A. 2010 Jun 4. PMID:20534443<ref>PMID:20534443</ref> |
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| - | | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | <!--
| + | </div> |
| - | The line below this paragraph, {{ABSTRACT_PUBMED_20534443}}, adds the Publication Abstract to the page
| + | <div class="pdbe-citations 3m8f" style="background-color:#fffaf0;"></div> |
| - | (as it appears on PubMed at http://www.pubmed.gov), where 20534443 is the PubMed ID number.
| + | == References == |
| - | -->
| + | <references/> |
| - | {{ABSTRACT_PUBMED_20534443}}
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==About this Structure== | + | [[Category: Bacillus thuringiensis serovar israelensis]] |
| - | 3M8F is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8F OCA].
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Ni L]] |
| - | ==Reference== | + | [[Category: Schumacher MA]] |
| - | <ref group="xtra">PMID:20534443</ref><references group="xtra"/> | + | |
| - | [[Category: Bacillus thuringiensis]] | + | |
| - | [[Category: Ni, L.]] | + | |
| - | [[Category: Schumacher, M A.]] | + | |
| - | [[Category: Dna binding protein]] | + | |
| - | [[Category: Plasmid segregation]]
| + | |
| - | [[Category: Tubr]]
| + | |
| - | [[Category: Winged helix-turn-helix]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 21 09:54:16 2010''
| + | |
| Structural highlights
Function
TUBR_BACTI A DNA-binding protein that is part of the type III plasmid partition system used to ensure correct segregation of the pBtoxis plasmid. Cooperatively binds to the centromere-like site (tubC), which may seed filament formation by the TubZ polymerizing GTPase, stabilizing TubZ filaments. TubR-tubC complexes track the depolymerizing minus end of the filament, probably pulling plasmid within the cell (PubMed:20534443, PubMed:23010931, PubMed:25825718). Required for plasmid replication (PubMed:16936050, PubMed:17873046). Negatively regulates levels of TubZ; its effect on RNA expression has not been shown (Probable). Specifically binds iterons, 12-bp imperfect direct repeats that function as a plasmid origin of replication (PubMed:17873046, PubMed:23010931, PubMed:25825718). Four TubR dimers bind to tubC, forming an extended bent DNA-protein filament with protein wrapping helically around the outside of the DNA (PubMed:20534443, PubMed:23010931).[1] [2] [3] [4] [5] [6]
Publication Abstract from PubMed
The segregation of plasmid DNA typically requires three elements: a DNA centromere site, an NTPase, and a centromere-binding protein. Because of their simplicity, plasmid partition systems represent tractable models to study the molecular basis of DNA segregation. Unlike eukaryotes, which utilize the GTPase tubulin to segregate DNA, the most common plasmid-encoded NTPases contain Walker-box and actin-like folds. Recently, a plasmid stability cassette on Bacillus thuringiensis pBtoxis encoding a putative FtsZ/tubulin-like NTPase called TubZ and DNA-binding protein called TubR has been described. How these proteins collaborate to impart plasmid stability, however, is unknown. Here we show that the TubR structure consists of an intertwined dimer with a winged helix-turn-helix (HTH) motif. Strikingly, however, the TubR recognition helices mediate dimerization, making canonical HTH-DNA interactions impossible. Mutagenesis data indicate that a basic patch, encompassing the two wing regions and the N termini of the recognition helices, mediates DNA binding, which indicates an unusual HTH-DNA interaction mode in which the N termini of the recognition helices insert into a single DNA groove and the wings into adjacent DNA grooves. The TubZ structure shows that it is as similar structurally to eukaryotic tubulin as it is to bacterial FtsZ. TubZ forms polymers with guanine nucleotide-binding characteristics and polymer dynamics similar to tubulin. Finally, we show that the exposed TubZ C-terminal region interacts with TubR-DNA, linking the TubR-bound pBtoxis to TubZ polymerization. The combined data suggest a mechanism for TubZ-polymer powered plasmid movement.
Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition.,Ni L, Xu W, Kumaraswami M, Schumacher MA Proc Natl Acad Sci U S A. 2010 Jun 4. PMID:20534443[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tang M, Bideshi DK, Park HW, Federici BA. Minireplicon from pBtoxis of Bacillus thuringiensis subsp. israelensis. Appl Environ Microbiol. 2006 Nov;72(11):6948-54. PMID:16936050 doi:10.1128/AEM.00976-06
- ↑ Tang M, Bideshi DK, Park HW, Federici BA. Iteron-binding ORF157 and FtsZ-like ORF156 proteins encoded by pBtoxis play a role in its replication in Bacillus thuringiensis subsp. israelensis. J Bacteriol. 2007 Nov;189(22):8053-8. PMID:17873046 doi:10.1128/JB.00908-07
- ↑ Ni L, Xu W, Kumaraswami M, Schumacher MA. Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition. Proc Natl Acad Sci U S A. 2010 Jun 4. PMID:20534443
- ↑ Aylett CH, Lowe J. Superstructure of the centromeric complex of TubZRC plasmid partitioning systems. Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16522-7. doi:, 10.1073/pnas.1210899109. Epub 2012 Sep 25. PMID:23010931 doi:http://dx.doi.org/10.1073/pnas.1210899109
- ↑ Fink G, Löwe J. Reconstitution of a prokaryotic minus end-tracking system using TubRC centromeric complexes and tubulin-like protein TubZ filaments. Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):E1845-50. PMID:25825718 doi:10.1073/pnas.1423746112
- ↑ Larsen RA, Cusumano C, Fujioka A, Lim-Fong G, Patterson P, Pogliano J. Treadmilling of a prokaryotic tubulin-like protein, TubZ, required for plasmid stability in Bacillus thuringiensis. Genes Dev. 2007 Jun 1;21(11):1340-52. PMID:17510284 doi:10.1101/gad.1546107
- ↑ Ni L, Xu W, Kumaraswami M, Schumacher MA. Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits the prokaryotic tubulin homolog TubZ to effect DNA partition. Proc Natl Acad Sci U S A. 2010 Jun 4. PMID:20534443
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