DTXR_CORDI
ID DTXR_CORDI Reviewed; 226 AA.
AC P0DJL7; P33120; Q5XQ41; Q5XQ42; Q5XQ43;
DT 05-SEP-2012, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2012, sequence version 1.
DT 03-AUG-2022, entry version 61.
DE RecName: Full=Diphtheria toxin repressor;
DE AltName: Full=Iron-dependent diphtheria tox regulatory element;
DE AltName: Full=Tox regulatory factor;
GN Name=dtxR; OrderedLocusNames=DIP1414;
OS Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype
OS gravis).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=257309;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=C7(-);
RX PubMed=2116013; DOI=10.1073/pnas.87.15.5968;
RA Boyd J.M., Oza M.N., Murphy J.R.;
RT "Molecular cloning and DNA sequence analysis of a diphtheria tox iron-
RT dependent regulatory element (dtxR) from Corynebacterium diphtheriae.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:5968-5972(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=1030(-), and C7hm723(-);
RX PubMed=1735717; DOI=10.1128/jb.174.4.1268-1272.1992;
RA Boyd J.M., Hall K.C., Murphy J.R.;
RT "DNA sequences and characterization of dtxR alleles from Corynebacterium
RT diphtheriae PW8(-), 1030(-), and C7hm723(-).";
RL J. Bacteriol. 174:1268-1272(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND STUDY OF FUNCTIONALITY.
RC STRAIN=CD95/211-, CD95/305-, and CD95/407-;
RX PubMed=15634975; DOI=10.1128/jcm.43.1.223-228.2005;
RA De Zoysa A.S., Efstratiou A., Hawkey P.M.;
RT "Molecular characterization of diphtheria toxin repressor (dtxR) genes
RT present in nontoxigenic Corynebacterium diphtheriae strains isolated in the
RT United Kingdom.";
RL J. Clin. Microbiol. 43:223-228(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700971 / NCTC 13129 / Biotype gravis;
RX PubMed=14602910; DOI=10.1093/nar/gkg874;
RA Cerdeno-Tarraga A.-M., Efstratiou A., Dover L.G., Holden M.T.G.,
RA Pallen M.J., Bentley S.D., Besra G.S., Churcher C.M., James K.D.,
RA De Zoysa A., Chillingworth T., Cronin A., Dowd L., Feltwell T., Hamlin N.,
RA Holroyd S., Jagels K., Moule S., Quail M.A., Rabbinowitsch E.,
RA Rutherford K.M., Thomson N.R., Unwin L., Whitehead S., Barrell B.G.,
RA Parkhill J.;
RT "The complete genome sequence and analysis of Corynebacterium diphtheriae
RT NCTC13129.";
RL Nucleic Acids Res. 31:6516-6523(2003).
RN [5]
RP CHARACTERIZATION.
RX PubMed=1502169; DOI=10.1073/pnas.89.16.7576;
RA Schmitt M.P., Twiddy E.M., Holmes R.K.;
RT "Purification and characterization of the diphtheria toxin repressor.";
RL Proc. Natl. Acad. Sci. U.S.A. 89:7576-7580(1992).
RN [6]
RP METAL-BINDING.
RX PubMed=1400485; DOI=10.1016/s0021-9258(19)36677-3;
RA Tao X., Murphy J.R.;
RT "Binding of the metalloregulatory protein DtxR to the diphtheria tox
RT operator requires a divalent heavy metal ion and protects the palindromic
RT sequence from DNase I digestion.";
RL J. Biol. Chem. 267:21761-21764(1992).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=8823163; DOI=10.1021/bi960861d;
RA Qiu X., Pohl E., Holmes R.K., Hol W.G.J.;
RT "High-resolution structure of the diphtheria toxin repressor complexed with
RT cobalt and manganese reveals an SH3-like third domain and suggests a
RT possible role of phosphate as co-corepressor.";
RL Biochemistry 35:12292-12302(1996).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RX PubMed=7568230; DOI=10.1073/pnas.92.21.9843;
RA Schiering N., Tao X., Zeng H., Murphy J.R., Petsko G.A., Ringe D.;
RT "Structures of the apo- and the metal ion-activated forms of the diphtheria
RT tox repressor from Corynebacterium diphtheriae.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:9843-9850(1995).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RX PubMed=9697776; DOI=10.1038/28893;
RA White A., Ding X., Vanderspek J.C., Murphy J.R., Ringe D.;
RT "Structure of the metal-ion-activated diphtheria toxin repressor/tox
RT operator complex.";
RL Nature 394:502-506(1998).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=10085021; DOI=10.1128/iai.67.4.1806-1811.1999;
RA Goranson-Siekierke J., Pohl E., Hol W.G.J., Holmes R.K.;
RT "Anion-coordinating residues at binding site 1 are essential for the
RT biological activity of the diphtheria toxin repressor.";
RL Infect. Immun. 67:1806-1811(1999).
RN [11]
RP STRUCTURE BY NMR OF 130-226.
RX PubMed=10339551; DOI=10.1073/pnas.96.11.6119;
RA Wang G., Wylie G.P., Twigg P.D., Caspar D.L.D., Murphy J.R., Logan T.M.;
RT "Solution structure and peptide binding studies of the C-terminal src
RT homology 3-like domain of the diphtheria toxin repressor protein.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:6119-6124(1999).
CC -!- FUNCTION: Iron-binding repressor of the dipheteria toxin gene
CC expression. May serve as a global regulator of gene expression.
CC Represses ripA under iron excess.
CC -!- SUBUNIT: Homodimer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- MISCELLANEOUS: The N-terminal region may be involved in iron binding
CC and may associate with the tox operator. Binding of dtxR to tox
CC operator requires a divalent metal ion such as cobalt, ferric,
CC manganese, and nickel ions whereas zinc ions show weak activation.
CC -!- MISCELLANEOUS: The dtxR gene was functional in the non-toxygenic
CC strains CD95/211-, CD95/305- and CD95/407- isolated in the United
CC Kingdom. These findings demonstrate that, if lysogenised by a
CC bacteriophage, non-toxygenic strains could produce toxin and therefore
CC represent a potential reservoir for toxygenic C.diphtheriae.
CC -!- SIMILARITY: Belongs to the DtxR/MntR family. {ECO:0000305}.
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DR EMBL; M34239; AAA23296.1; -; Genomic_DNA.
DR EMBL; M80336; AAA23302.1; -; Genomic_DNA.
DR EMBL; M80337; AAA23301.1; -; Genomic_DNA.
DR EMBL; AY741368; AAU93781.1; -; Genomic_DNA.
DR EMBL; AY741369; AAU93782.1; -; Genomic_DNA.
DR EMBL; AY741370; AAU93783.1; -; Genomic_DNA.
DR EMBL; BX248358; CAE49945.1; -; Genomic_DNA.
DR PIR; A35968; A35968.
DR RefSeq; WP_010935052.1; NC_002935.2.
DR PDB; 1BI0; X-ray; 2.30 A; A=1-226.
DR PDB; 1BI1; X-ray; 2.20 A; A=1-226.
DR PDB; 1BI2; X-ray; 2.30 A; A/B=1-226.
DR PDB; 1BI3; X-ray; 2.40 A; A/B=1-226.
DR PDB; 1BYM; NMR; -; A=130-226.
DR PDB; 1C0W; X-ray; 3.20 A; A/B/C/D=2-226.
DR PDB; 1DDN; X-ray; 3.00 A; A/B/C/D=1-226.
DR PDB; 1DPR; X-ray; 3.00 A; A/B=1-226.
DR PDB; 1F5T; X-ray; 3.00 A; A/B/C/D=1-121.
DR PDB; 1FWZ; X-ray; 2.30 A; A=1-226.
DR PDB; 1G3S; X-ray; 2.40 A; A=1-226.
DR PDB; 1G3T; X-ray; 2.35 A; A/B=1-226.
DR PDB; 1G3W; X-ray; 2.40 A; A=1-226.
DR PDB; 1G3Y; X-ray; 2.80 A; A=1-226.
DR PDB; 1P92; X-ray; 2.10 A; A=1-226.
DR PDB; 1QVP; NMR; -; A=148-226.
DR PDB; 1QW1; NMR; -; A=110-226.
DR PDB; 1XCV; X-ray; 2.10 A; A=1-139.
DR PDB; 2DTR; X-ray; 1.90 A; A=1-226.
DR PDB; 2QQ9; X-ray; 1.71 A; A=1-226.
DR PDB; 2QQA; X-ray; 2.10 A; A=1-226.
DR PDB; 2QQB; X-ray; 1.92 A; A=1-226.
DR PDB; 2TDX; X-ray; 2.40 A; A=1-226.
DR PDB; 3GLX; X-ray; 1.85 A; A=1-226.
DR PDBsum; 1BI0; -.
DR PDBsum; 1BI1; -.
DR PDBsum; 1BI2; -.
DR PDBsum; 1BI3; -.
DR PDBsum; 1BYM; -.
DR PDBsum; 1C0W; -.
DR PDBsum; 1DDN; -.
DR PDBsum; 1DPR; -.
DR PDBsum; 1F5T; -.
DR PDBsum; 1FWZ; -.
DR PDBsum; 1G3S; -.
DR PDBsum; 1G3T; -.
DR PDBsum; 1G3W; -.
DR PDBsum; 1G3Y; -.
DR PDBsum; 1P92; -.
DR PDBsum; 1QVP; -.
DR PDBsum; 1QW1; -.
DR PDBsum; 1XCV; -.
DR PDBsum; 2DTR; -.
DR PDBsum; 2QQ9; -.
DR PDBsum; 2QQA; -.
DR PDBsum; 2QQB; -.
DR PDBsum; 2TDX; -.
DR PDBsum; 3GLX; -.
DR AlphaFoldDB; P0DJL7; -.
DR BMRB; P0DJL7; -.
DR SMR; P0DJL7; -.
DR MINT; P0DJL7; -.
DR STRING; 257309.DIP1414; -.
DR PRIDE; P0DJL7; -.
DR EnsemblBacteria; CAE49945; CAE49945; DIP1414.
DR KEGG; cdi:DIP1414; -.
DR HOGENOM; CLU_069532_0_0_11; -.
DR OMA; NIIPACD; -.
DR OrthoDB; 2047422at2; -.
DR Proteomes; UP000002198; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
DR GO; GO:0042802; F:identical protein binding; IPI:CAFA.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0017124; F:SH3 domain binding; IMP:CAFA.
DR GO; GO:0046914; F:transition metal ion binding; IEA:InterPro.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 1.10.60.10; -; 1.
DR Gene3D; 2.30.30.90; -; 1.
DR InterPro; IPR040767; DtxR_SH3.
DR InterPro; IPR007167; Fe-transptr_FeoA.
DR InterPro; IPR001367; Fe_dep_repressor.
DR InterPro; IPR036421; Fe_dep_repressor_sf.
DR InterPro; IPR038157; FeoA_core_dom.
DR InterPro; IPR022687; HTH_DTXR.
DR InterPro; IPR022689; Iron_dep_repressor.
DR InterPro; IPR008988; Transcriptional_repressor_C.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR Pfam; PF18357; DtxR; 1.
DR Pfam; PF02742; Fe_dep_repr_C; 1.
DR Pfam; PF01325; Fe_dep_repress; 1.
DR SMART; SM00899; FeoA; 1.
DR SMART; SM00529; HTH_DTXR; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR SUPFAM; SSF47979; SSF47979; 1.
DR SUPFAM; SSF50037; SSF50037; 1.
DR PROSITE; PS50944; HTH_DTXR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA-binding; Iron; Reference proteome; Repressor;
KW Transcription; Transcription regulation.
FT CHAIN 1..226
FT /note="Diphtheria toxin repressor"
FT /id="PRO_0000201106"
FT DOMAIN 4..65
FT /note="HTH dtxR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00296"
FT VARIANT 47
FT /note="R -> H (in iron-insensitive tox constitutive mutant
FT C7hm723)"
FT VARIANT 141
FT /note="G -> R (in strain: CD95/211-)"
FT VARIANT 147
FT /note="V -> A (in strain: C7(-), C7hm723(-), 1030(-), CD95/
FT 305-, CD95/211- and CD95/407-)"
FT VARIANT 165
FT /note="I -> V (in strain: 1030(-))"
FT VARIANT 174
FT /note="V -> A (in strain: 1030(-))"
FT VARIANT 191
FT /note="S -> T (in strain: 1030(-))"
FT VARIANT 199
FT /note="D -> V (in strain: CD95/407-)"
FT VARIANT 201
FT /note="H -> R (in strain: CD95/305-)"
FT VARIANT 205
FT /note="S -> R (in strain: 1030(-))"
FT VARIANT 214
FT /note="I -> L (in strain: C7(-), C7hm723(-), CD95/305-,
FT CD95/211- and CD95/407-)"
FT VARIANT 214
FT /note="I -> Y (in strain: 1030(-))"
FT VARIANT 218
FT /note="A -> T (in strain: 1030(-))"
FT VARIANT 221
FT /note="I -> M (in strain: CD95/211-)"
FT VARIANT 221
FT /note="I -> T (in strain: CD95/407-)"
FT HELIX 4..21
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 27..34
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 38..50
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 53..56
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 60..64
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 66..88
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 94..104
FT /evidence="ECO:0007829|PDB:2QQ9"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 110..119
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 127..130
FT /evidence="ECO:0007829|PDB:1DPR"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 145..148
FT /evidence="ECO:0007829|PDB:1QW1"
FT STRAND 149..151
FT /evidence="ECO:0007829|PDB:2QQA"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 161..167
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 177..184
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 188..195
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:1P92"
FT STRAND 203..208
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 210..212
FT /evidence="ECO:0007829|PDB:2QQ9"
FT HELIX 215..220
FT /evidence="ECO:0007829|PDB:2QQ9"
FT STRAND 222..224
FT /evidence="ECO:0007829|PDB:2QQ9"
SQ SEQUENCE 226 AA; 25344 MW; A14F89FDB8719D5C CRC64;
MKDLVDTTEM YLRTIYELEE EGVTPLRARI AERLEQSGPT VSQTVARMER DGLVVVASDR
SLQMTPTGRT LATAVMRKHR LAERLLTDII GLDINKVHDE ACRWEHVMSD EVERRLVKVL
KDVSRSPFGN PIPGLDELGV GNSDAAVPGT RVIDAATSMP RKVRIVQINE IFQVETDQFT
QLLDADIRVG SEVEIVDRDG HITLSHNGKD VELIDDLAHT IRIEEL
