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3m8f

From Proteopedia

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Current revision

Protein structure of type III plasmid segregation TubR mutant

Structural highlights

3m8f is a 2 chain structure with sequence from Bacillus thuringiensis serovar israelensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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/3m8f"

Categories: Bacillus thuringiensis serovar israelensis | Large Structures | Ni L | Schumacher MA

@@ Line 3: / Line 3: @@
 <StructureSection load='3m8f' size='340' side='right'caption='[[3m8f]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3m8f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacti Bacti]. 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>
+<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>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3m89|3m89]], [[3m8e|3m8e]], [[3m8k|3m8k]]</div></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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pBt157 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1430 BACTI])</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>
 </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 ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacti]]
+[[Category: Bacillus thuringiensis serovar israelensis]]
 [[Category: Large Structures]]
-[[Category: Ni, L]]
+[[Category: Ni L]]
-[[Category: Schumacher, M A]]
+[[Category: Schumacher MA]]
-[[Category: Dna binding protein]]
-[[Category: Plasmid segregation]]
-[[Category: Tubr]]
-[[Category: Winged helix-turn-helix]]

3m8f

From Proteopedia

Current revision

Protein structure of type III plasmid segregation TubR mutant

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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