TUBR_BACTI
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 25-MAY-2022, entry version 73.
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; Firmicutes; 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}.
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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; -; 1.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR SUPFAM; SSF46785; SSF46785; 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
