ID   TUBR_BACTI              Reviewed;         104 AA.
AC   Q8KNP2;
DT   13-NOV-2019, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2002, sequence version 1.
DT   03-MAY-2023, entry version 76.
DE   RecName: Full=DNA-binding transcriptional repressor TubR {ECO:0000303|PubMed:17510284, ECO:0000305};
GN   Name=tubR {ECO:0000303|PubMed:17510284}; Synonyms=pBt157;
GN   ORFNames=ATN07_33545;
OS   Bacillus thuringiensis subsp. israelensis.
OG   Plasmid pAM65-52-4-128K {ECO:0000303|PubMed:27810477},
OG   Plasmid pBtoxis {ECO:0000303|PubMed:12324359}, and
OG   Plasmid pT0124-4 {ECO:0000303|Ref.3}.
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC   Bacillus cereus group.
OX   NCBI_TaxID=1430;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=4Q2-72 / 4Q5; PLASMID=pBtoxis;
RX   PubMed=12324359; DOI=10.1128/aem.68.10.5082-5095.2002;
RA   Berry C., O'Niel S., Ben-Dov E., Jones A.F., Murphy L., Quail M.A.,
RA   Harris D., Zaritsky A., Parkhill J.;
RT   "Complete sequence and organization of pBtoxis, the toxin-coding plasmid of
RT   Bacillus thuringiensis subsp. israelensis.";
RL   Appl. Environ. Microbiol. 68:5082-5095(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=AM65-52; PLASMID=pAM65-52-4-128K;
RX   PubMed=27810477; DOI=10.1016/j.resmic.2016.10.008;
RA   Bolotin A., Gillis A., Sanchis V., Nielsen-LeRoux C., Mahillon J.,
RA   Lereclus D., Sorokin A.;
RT   "Comparative genomics of extrachromosomal elements in Bacillus
RT   thuringiensis subsp. israelensis.";
RL   Res. Microbiol. 168:331-344(2017).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=1.24; PLASMID=pT0124-4;
RA   Alves G.B., Melo F.L., Campos F.S., Correa R.F.T., Ribeiro B.M.,
RA   Aguiar R.W.S.;
RT   "Bacillus turingiensis from Tocantins.";
RL   Submitted (DEC-2016) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   FUNCTION, PROBABLE OPERON, DISRUPTION PHENOTYPE, AND BIOTECHNOLOGY.
RC   STRAIN=4Q5; PLASMID=pBtoxis;
RX   PubMed=16936050; DOI=10.1128/aem.00976-06;
RA   Tang M., Bideshi D.K., Park H.W., Federici B.A.;
RT   "Minireplicon from pBtoxis of Bacillus thuringiensis subsp. israelensis.";
RL   Appl. Environ. Microbiol. 72:6948-6954(2006).
RN   [5]
RP   FUNCTION, PROBABLE OPERON, AND DISRUPTION PHENOTYPE.
RC   STRAIN=ATCC 35646 / USDA HD522; PLASMID=pBtoxis;
RX   PubMed=17510284; DOI=10.1101/gad.1546107;
RA   Larsen R.A., Cusumano C., Fujioka A., Lim-Fong G., Patterson P.,
RA   Pogliano J.;
RT   "Treadmilling of a prokaryotic tubulin-like protein, TubZ, required for
RT   plasmid stability in Bacillus thuringiensis.";
RL   Genes Dev. 21:1340-1352(2007).
RN   [6]
RP   FUNCTION, INTERACTION WITH TUBZ, SUBUNIT, DISRUPTION PHENOTYPE, AND
RP   DNA-BINDING.
RC   STRAIN=4Q5; PLASMID=pBtoxis;
RX   PubMed=17873046; DOI=10.1128/jb.00908-07;
RA   Tang M., Bideshi D.K., Park H.W., Federici B.A.;
RT   "Iteron-binding ORF157 and FtsZ-like ORF156 proteins encoded by pBtoxis
RT   play a role in its replication in Bacillus thuringiensis subsp.
RT   israelensis.";
RL   J. Bacteriol. 189:8053-8058(2007).
RN   [7]
RP   FUNCTION, SUBUNIT, AND DNA-BINDING.
RC   PLASMID=pBtoxis;
RX   PubMed=25825718; DOI=10.1073/pnas.1423746112;
RA   Fink G., Loewe J.;
RT   "Reconstitution of a prokaryotic minus end-tracking system using TubRC
RT   centromeric complexes and tubulin-like protein TubZ filaments.";
RL   Proc. Natl. Acad. Sci. U.S.A. 112:E1845-E1850(2015).
RN   [8] {ECO:0007744|PDB:3M8E, ECO:0007744|PDB:3M8F, ECO:0007744|PDB:3M9A}
RP   X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS), FUNCTION, SUBUNIT, MUTAGENESIS OF
RP   LYS-43; SER-63; ALA-67; ARG-74; ARG-77 AND LYS-79, AND DNA-BINDING.
RC   PLASMID=pBtoxis;
RX   PubMed=20534443; DOI=10.1073/pnas.1003817107;
RA   Ni L., Xu W., Kumaraswami M., Schumacher M.A.;
RT   "Plasmid protein TubR uses a distinct mode of HTH-DNA binding and recruits
RT   the prokaryotic tubulin homolog TubZ to effect DNA partition.";
RL   Proc. Natl. Acad. Sci. U.S.A. 107:11763-11768(2010).
RN   [9] {ECO:0007744|PDB:4ASO, ECO:0007744|PDB:4ASS}
RP   X-RAY CRYSTALLOGRAPHY (7.00 ANGSTROMS) IN COMPLEX WITH DNA, SUBUNIT, AND
RP   DNA-BINDING.
RX   PubMed=23010931; DOI=10.1073/pnas.1210899109;
RA   Aylett C.H., Lowe J.;
RT   "Superstructure of the centromeric complex of TubZRC plasmid partitioning
RT   systems.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:16522-16527(2012).
CC   -!- FUNCTION: A DNA-binding protein that is part of the type III plasmid
CC       partition system used to ensure correct segregation of the pBtoxis
CC       plasmid. Cooperatively binds to the centromere-like site (tubC), which
CC       may seed filament formation by the TubZ polymerizing GTPase,
CC       stabilizing TubZ filaments. TubR-tubC complexes track the
CC       depolymerizing minus end of the filament, probably pulling plasmid
CC       within the cell (PubMed:20534443, PubMed:23010931, PubMed:25825718).
CC       Required for plasmid replication (PubMed:16936050, PubMed:17873046).
CC       Negatively regulates levels of TubZ; its effect on RNA expression has
CC       not been shown (Probable). Specifically binds iterons, 12-bp imperfect
CC       direct repeats that function as a plasmid origin of replication
CC       (PubMed:17873046, PubMed:23010931, PubMed:25825718). Four TubR dimers
CC       bind to tubC, forming an extended bent DNA-protein filament with
CC       protein wrapping helically around the outside of the DNA
CC       (PubMed:20534443, PubMed:23010931). {ECO:0000269|PubMed:16936050,
CC       ECO:0000269|PubMed:17873046, ECO:0000269|PubMed:20534443,
CC       ECO:0000269|PubMed:23010931, ECO:0000269|PubMed:25825718,
CC       ECO:0000305|PubMed:17510284}.
CC   -!- SUBUNIT: Homodimer (PubMed:20534443, PubMed:23010931). Binds to tubC
CC       DNA, the TubR-DNA complex binds to TubZ (PubMed:17873046,
CC       PubMed:20534443). {ECO:0000269|PubMed:17873046,
CC       ECO:0000269|PubMed:20534443, ECO:0000269|PubMed:23010931}.
CC   -!- INTERACTION:
CC       Q8KNP2; Q8KNP2: tubR; NbExp=2; IntAct=EBI-15857953, EBI-15857953;
CC   -!- INDUCTION: Probably part of the tubR-tubZ operon.
CC       {ECO:0000305|PubMed:16936050, ECO:0000305|PubMed:17510284}.
CC   -!- DOMAIN: Although this has the same function as TubR of B.cereus strain
CC       ATCC 10987 there is little sequence homology and the dimerization
CC       interface is different. {ECO:0000305}.
CC   -!- DISRUPTION PHENOTYPE: Loss of plasmid replication (PubMed:16936050,
CC       PubMed:17873046). TubZ levels increase, TubZ still polymerizes
CC       (PubMed:17510284). {ECO:0000269|PubMed:16936050,
CC       ECO:0000269|PubMed:17510284, ECO:0000269|PubMed:17873046}.
CC   -!- BIOTECHNOLOGY: A miniplasmid containing this and downstream gene tubZ
CC       is able to replicate in B.thuringiensis subsp. israelensis and express
CC       insect toxin proteins. The miniplasmid could be used to make plasmids
CC       for insect toxin overexpression. {ECO:0000269|PubMed:16936050}.
CC   -!- MISCELLANEOUS: The pBtoxis plasmid encodes all the major endotoxin
CC       proteins (Cyt1Aa, Cry4Aa, Cry4Ba, and Cry11Aa) responsible for the
CC       mosquito larvicidal activity of strain 4Q2.
CC       {ECO:0000305|PubMed:12324359}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AL731825; CAD30187.1; -; Genomic_DNA.
DR   EMBL; CP013279; AND28645.1; -; Genomic_DNA.
DR   EMBL; KY352353; ASO64581.1; -; Genomic_DNA.
DR   RefSeq; WP_001078053.1; NZ_VEIF01000064.1.
DR   RefSeq; YP_001573871.1; NC_010076.1.
DR   PDB; 3M8E; X-ray; 2.00 A; A/B=1-104.
DR   PDB; 3M8F; X-ray; 2.80 A; A/B=1-104.
DR   PDB; 3M9A; X-ray; 2.50 A; A=1-104.
DR   PDB; 4ASO; X-ray; 7.00 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=1-104.
DR   PDB; 4ASS; X-ray; 7.00 A; A/B/C/D/E/F/G/H/I=1-104.
DR   PDBsum; 3M8E; -.
DR   PDBsum; 3M8F; -.
DR   PDBsum; 3M9A; -.
DR   PDBsum; 4ASO; -.
DR   PDBsum; 4ASS; -.
DR   AlphaFoldDB; Q8KNP2; -.
DR   SMR; Q8KNP2; -.
DR   DIP; DIP-59347N; -.
DR   IntAct; Q8KNP2; 1.
DR   EvolutionaryTrace; Q8KNP2; -.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0030541; P:plasmid partitioning; IEA:UniProtKB-KW.
DR   Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 1.
DR   InterPro; IPR036388; WH-like_DNA-bd_sf.
DR   InterPro; IPR036390; WH_DNA-bd_sf.
DR   SUPFAM; SSF46785; Winged helix' DNA-binding domain; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA-binding; Plasmid; Plasmid partition; Repressor;
KW   Transcription; Transcription regulation.
FT   CHAIN           1..104
FT                   /note="DNA-binding transcriptional repressor TubR"
FT                   /id="PRO_0000448567"
FT   DNA_BIND        43..50
FT                   /note="HTH"
FT                   /evidence="ECO:0000305|PubMed:16936050"
FT   DNA_BIND        54..65
FT                   /note="HTH"
FT                   /evidence="ECO:0000305|PubMed:16936050"
FT   MUTAGEN         43
FT                   /note="K->A: No DNA binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   MUTAGEN         63
FT                   /note="S->R: No longer dimerizes, decreased DNA-binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   MUTAGEN         63
FT                   /note="S->W: Dimerizes, decreased DNA binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   MUTAGEN         67
FT                   /note="A->R: No longer dimerizes, decreased DNA binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   MUTAGEN         67
FT                   /note="A->W: Dimerizes, decreased DNA binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   MUTAGEN         74
FT                   /note="R->A: No DNA binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   MUTAGEN         77
FT                   /note="R->A: No DNA binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   MUTAGEN         79
FT                   /note="K->A: Decreased DNA binding."
FT                   /evidence="ECO:0000269|PubMed:20534443"
FT   STRAND          7..10
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   HELIX           11..19
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   HELIX           22..30
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   HELIX           43..48
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   STRAND          50..52
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   HELIX           54..66
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   STRAND          69..75
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   STRAND          78..83
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   HELIX           85..92
FT                   /evidence="ECO:0007829|PDB:3M8E"
FT   TURN            93..96
FT                   /evidence="ECO:0007829|PDB:3M8E"
SQ   SEQUENCE   104 AA;  11828 MW;  E1296C5D811139B5 CRC64;
     MNRDHFYTLN IAEIAERIGN DDCAYQVLMA FINENGEAQM LNKTAVAEMI QLSKPTVFAT
     VNSFYCAGYI DETRVGRSKI YTLSDLGVEI VECFKQKAME MRNL
//