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Volumn 292, Issue 3, 1999, Pages 653-667

Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain

Author keywords

Crystal structure; DtxR; Iron dependent regulator; Protein DNA complex

Indexed keywords

COBALT; DIMER; DIPHTHERIA TOXIN; REGULATOR PROTEIN; SIDEROPHORE;

EID: 0000868851     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3073     Document Type: Article
Times cited : (113)

References (50)
  • 1
    • 0000913086 scopus 로고
    • A fast algorithm for rendering space filling molecule pictures
    • Bacon D. J., Anderson W. F. A fast algorithm for rendering space filling molecule pictures. J. Mol. Graph. 6:1988;219-220.
    • (1988) J. Mol. Graph. , vol.6 , pp. 219-220
    • Bacon, D.J.1    Anderson, W.F.2
  • 2
    • 0023576859 scopus 로고
    • Molecular mechanism of the regulation of siderophore-mediated iron-assimilation
    • Bagg A., Neilands J. B. Molecular mechanism of the regulation of siderophore-mediated iron-assimilation. Microbiol. Rev. 51:1987;509-518.
    • (1987) Microbiol. Rev. , vol.51 , pp. 509-518
    • Bagg, A.1    Neilands, J.B.2
  • 3
    • 0025300518 scopus 로고
    • Molecular cloning and DNA sequence analysis of a diphtheria- tox iron-dependent regulatory (dtxR) element from Corynebacterium diphtheriae
    • Boyd J. M., Oza M., Murphy J. R. Molecular cloning and DNA sequence analysis of a diphtheria- tox iron-dependent regulatory (dtxR) element from Corynebacterium diphtheriae. Proc. Natl Acad. Sci. USA. 87:1990;5968-5972.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 5968-5972
    • Boyd, J.M.1    Oza, M.2    Murphy, J.R.3
  • 4
    • 0030861787 scopus 로고    scopus 로고
    • Avoidance of iron toxicity through regulation of bacterial iron transport
    • Braun V. Avoidance of iron toxicity through regulation of bacterial iron transport. Biol. Chem. 387:1997;779-786.
    • (1997) Biol. Chem. , vol.387 , pp. 779-786
    • Braun, V.1
  • 5
    • 0031569798 scopus 로고    scopus 로고
    • The crystal structure of an intact human Max-DNA complex: New insights into mechanisms of transcriptional control
    • Brownlie P., Ceska T. A., Lamers M., Romier C., Stier G., Teo H., Suck D. The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control. Structure. 5:1997;509-520.
    • (1997) Structure , vol.5 , pp. 509-520
    • Brownlie, P.1    Ceska, T.A.2    Lamers, M.3    Romier, C.4    Stier, G.5    Teo, H.6    Suck, D.7
  • 6
    • 0001897686 scopus 로고
    • Assessment of phase accuracy by cross validation: The free R -value, methods and applications
    • Brünger A. T. Assessment of phase accuracy by cross validation: the free R -value, methods and applications. Acta Crystallog. sect. D. 49:1993;24-36.
    • (1993) Acta Crystallog. Sect. D , vol.49 , pp. 24-36
    • Brünger, A.T.1
  • 8
    • 84901961522 scopus 로고
    • Slow-cooling protocols for crystallographic refinement by simulated annealing
    • Brünger A. T., Krukowski A., Erickson J. W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallog. sect. A. 46:1990;585-593.
    • (1990) Acta Crystallog. Sect. a , vol.46 , pp. 585-593
    • Brünger, A.T.1    Krukowski, A.2    Erickson, J.W.3
  • 9
    • 0026472376 scopus 로고
    • Iron metabolism-new perspectives in view
    • Crichton R. R., Ward R. J. Iron metabolism-new perspectives in view. Biochemistry. 31:1992;11255-11264.
    • (1992) Biochemistry , vol.31 , pp. 11255-11264
    • Crichton, R.R.1    Ward, R.J.2
  • 10
    • 0029964556 scopus 로고    scopus 로고
    • Identification of the primary metal ion-activation sites of the diphtheria tox repressor by X-ray crystallography and site-directed mutational analysis
    • Ding X., Zeng H., Schiering N., Ringe D., Murphy J. R. Identification of the primary metal ion-activation sites of the diphtheria tox repressor by X-ray crystallography and site-directed mutational analysis. Nature Struct. Biol. 3:1996;382-387.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 382-387
    • Ding, X.1    Zeng, H.2    Schiering, N.3    Ringe, D.4    Murphy, J.R.5
  • 12
    • 0032167951 scopus 로고    scopus 로고
    • Interdependence of mycobacterial iron regulation, oxidative-stress response and isoniazid resistance
    • Dussurget O., Smith I. Interdependence of mycobacterial iron regulation, oxidative-stress response and isoniazid resistance. Trends Microbiol. 6:1998;354-358.
    • (1998) Trends Microbiol. , vol.6 , pp. 354-358
    • Dussurget, O.1    Smith, I.2
  • 13
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
    • Esnouf R. M. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model. 15:1997;132-134.
    • (1997) J. Mol. Graph. Model. , vol.15 , pp. 132-134
    • Esnouf, R.M.1
  • 14
    • 0033051018 scopus 로고    scopus 로고
    • Anion-coordinating residues at binding site 1 are essential for the biological activity of the diphtheria toxin repressor (DtxR)
    • Goranson-Siekierke J., Pohl E., Hol W. G. J., Holmes R. K. Anion-coordinating residues at binding site 1 are essential for the biological activity of the diphtheria toxin repressor (DtxR). Infect. Immun. 67:1998;1806-1811.
    • (1998) Infect. Immun. , vol.67 , pp. 1806-1811
    • Goranson-Siekierke, J.1    Pohl, E.2    Hol, W.G.J.3    Holmes, R.K.4
  • 15
    • 0028858577 scopus 로고
    • Cloning and sequence analysis of the Corynebacterium diphtheriae dtxR homologue from Streptomyces lividans and S. pilosus encoding a putative iron repressor protein
    • Günther-Seeboth K., Schupp T. Cloning and sequence analysis of the Corynebacterium diphtheriae dtxR homologue from Streptomyces lividans and S. pilosus encoding a putative iron repressor protein. Gene. 166:1995;117-119.
    • (1995) Gene , vol.166 , pp. 117-119
    • Günther-Seeboth, K.1    Schupp, T.2
  • 16
    • 0021978310 scopus 로고
    • The role of the α-helix dipole in protein structure and function
    • Hol W. G. J. The role of the α-helix dipole in protein structure and function. Prog. Biophys. Mol. Biol. 45:1985;149-195.
    • (1985) Prog. Biophys. Mol. Biol. , vol.45 , pp. 149-195
    • Hol, W.G.J.1
  • 17
    • 0028172551 scopus 로고
    • Protein hydration observed by X-ray diffraction
    • Jing J.-S., Brünger A. T. Protein hydration observed by X-ray diffraction. J. Mol. Biol. 243:1994;100-115.
    • (1994) J. Mol. Biol. , vol.243 , pp. 100-115
    • Jing, J.-S.1    Brünger, A.T.2
  • 18
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
    • (1991) Acta Crystallog. Sect. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 19
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;964-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 964-950
    • Kraulis, P.1
  • 20
    • 0030879821 scopus 로고    scopus 로고
    • Identification and characterization of three new promoter/operators from Corynebacterium diphtheriae that are regulated by the diphtheria toxin repressor (DtxR) and iron
    • Lee J. H., Wang T., Ault K., Liu J., Schmitt M. P., Holmes R. K. Identification and characterization of three new promoter/operators from Corynebacterium diphtheriae that are regulated by the diphtheria toxin repressor (DtxR) and iron. Infect. Immun. 65:1997;4273-4280.
    • (1997) Infect. Immun. , vol.65 , pp. 4273-4280
    • Lee, J.H.1    Wang, T.2    Ault, K.3    Liu, J.4    Schmitt, M.P.5    Holmes, R.K.6
  • 21
    • 0027230853 scopus 로고
    • Role of iron in the regulation of virulence genes
    • Litwin C. M., Calderwood S. B. Role of iron in the regulation of virulence genes. Clin. Microbiol. Rev. 6:1993;137-149.
    • (1993) Clin. Microbiol. Rev. , vol.6 , pp. 137-149
    • Litwin, C.M.1    Calderwood, S.B.2
  • 22
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews B. W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497.
    • (1968) J. Mol. Biol. , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 23
    • 0028057108 scopus 로고
    • Raster3D Version 2.0-a program for photorealistic molecular graphics
    • Merritt E. A., Murphy M. E. P. Raster3D Version 2.0-a program for photorealistic molecular graphics. Acta Crystallog. sect. D. 50:1994;869-873.
    • (1994) Acta Crystallog. Sect. D , vol.50 , pp. 869-873
    • Merritt, E.A.1    Murphy, M.E.P.2
  • 24
    • 0028070009 scopus 로고
    • The role of iron-binding proteins in the survival of pathogenic bacteria
    • Mietzner T. A., Morse S. A. The role of iron-binding proteins in the survival of pathogenic bacteria. Annu. Rev. Nutr. 14:1995;471-493.
    • (1995) Annu. Rev. Nutr. , vol.14 , pp. 471-493
    • Mietzner, T.A.1    Morse, S.A.2
  • 25
    • 84920325457 scopus 로고
    • AMoRe, an automated package for molecular replacement
    • Navazza J. AMoRe, an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
    • (1994) Acta Crystallog. Sect. a , vol.50 , pp. 157-163
    • Navazza, J.1
  • 26
    • 0028855065 scopus 로고
    • Molecular cloning, DNA-sequence analysis, and characterization of the Corynebacterium diphtheriae dtxR homolog from Brevibacterium lactofermentum
    • Oguiza J. A., Tao X., Marcos A. T., Martin J. F., Murphy J. R. Molecular cloning, DNA-sequence analysis, and characterization of the Corynebacterium diphtheriae dtxR homolog from Brevibacterium lactofermentum. J. Bacteriol. 177:1995;465-467.
    • (1995) J. Bacteriol. , vol.177 , pp. 465-467
    • Oguiza, J.A.1    Tao, X.2    Marcos, A.T.3    Martin, J.F.4    Murphy, J.R.5
  • 27
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 29
    • 0030902083 scopus 로고    scopus 로고
    • Comparison of the high resolution structures of the diphtheria toxin repressor in complex with cobalt and zinc at the cation-anion binding site
    • Pohl E., Qiu X., Must L. M., Holmes R. K., Hol W. G. J. Comparison of the high resolution structures of the diphtheria toxin repressor in complex with cobalt and zinc at the cation-anion binding site. Protein Sci. 6:1997;1114-1118.
    • (1997) Protein Sci. , vol.6 , pp. 1114-1118
    • Pohl, E.1    Qiu, X.2    Must, L.M.3    Holmes, R.K.4    Hol, W.G.J.5
  • 30
    • 0032575642 scopus 로고    scopus 로고
    • Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor revealed in the crystal structures of apo- and holo-DtxR
    • Pohl E., Holmes R. K., Hol W. G. J. Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor revealed in the crystal structures of apo- and holo-DtxR. J. Biol. Chem. 35:1998;22420-22427.
    • (1998) J. Biol. Chem. , vol.35 , pp. 22420-22427
    • Pohl, E.1    Holmes, R.K.2    Hol, W.G.J.3
  • 31
    • 0001590980 scopus 로고    scopus 로고
    • Crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied
    • Pohl E., Holmes R. K., Hol W. G. J. Crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied. J. Mol. Biol. 285:1999;1145-1156.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1145-1156
    • Pohl, E.1    Holmes, R.K.2    Hol, W.G.J.3
  • 32
    • 0028993911 scopus 로고
    • Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation corepressors
    • Qiu X., Verlinde C. J. L. M., Zhang Z., Schmitt M. P., Holmes R. K., Hol W. G. J. Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation corepressors. Structure. 3:1995;87-100.
    • (1995) Structure , vol.3 , pp. 87-100
    • Qiu, X.1    Verlinde, C.J.L.M.2    Zhang, Z.3    Schmitt, M.P.4    Holmes, R.K.5    Hol, W.G.J.6
  • 33
    • 0029739483 scopus 로고    scopus 로고
    • High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor
    • Qiu X., Pohl E., Holmes R. K., Hol W. G. J. High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor. Biochemistry. 35:1996;12292-12302.
    • (1996) Biochemistry , vol.35 , pp. 12292-12302
    • Qiu, X.1    Pohl, E.2    Holmes, R.K.3    Hol, W.G.J.4
  • 34
    • 84944812409 scopus 로고
    • Improved Fourier coefficients for maps using phases from partial structures with errors
    • Read R. J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog. sect. A. 42:1986;140-149.
    • (1986) Acta Crystallog. Sect. a , vol.42 , pp. 140-149
    • Read, R.J.1
  • 35
    • 0028070557 scopus 로고
    • Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic refinement
    • Rice L. M., Brünger A. T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic refinement. Proteins: Struct. Funct. Genet. 19:1994;277-290.
    • (1994) Proteins: Struct. Funct. Genet. , vol.19 , pp. 277-290
    • Rice, L.M.1    Brünger, A.T.2
  • 36
    • 0028826149 scopus 로고
    • Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae
    • Schiering N., Tao X., Zeng H., Murphy J. R., Petsko G. A., Ringe D. Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae. Proc. Natl Acad. Sci. USA. 92:1995;9843-9850.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 9843-9850
    • Schiering, N.1    Tao, X.2    Zeng, H.3    Murphy, J.R.4    Petsko, G.A.5    Ringe, D.6
  • 37
    • 0030732290 scopus 로고    scopus 로고
    • Transcription of the Corynebacterium diphtheriae hmu0 gene is regulated by iron and heme
    • Schmitt M. P. Transcription of the Corynebacterium diphtheriae hmu0 gene is regulated by iron and heme. Infect. Immun. 65:1997;4634-4641.
    • (1997) Infect. Immun. , vol.65 , pp. 4634-4641
    • Schmitt, M.P.1
  • 38
    • 0025999830 scopus 로고
    • Characterization of a defective diphtheria toxin repressor (dtxR) allele and analysis of dtxR transcription in wild-type and mutant strains of Corynebacterium diphtheriae
    • Schmitt M. P., Holmes R. K. Characterization of a defective diphtheria toxin repressor (dtxR) allele and analysis of dtxR transcription in wild-type and mutant strains of Corynebacterium diphtheriae. Infect. Immun. 59:1991;3903-3908.
    • (1991) Infect. Immun. , vol.59 , pp. 3903-3908
    • Schmitt, M.P.1    Holmes, R.K.2
  • 39
    • 0027210121 scopus 로고
    • Analysis of diphtheria toxin repressor-operator interactions and characterization of a mutant with decreased binding activity for divalent metals
    • Schmitt M. P., Holmes R. K. Analysis of diphtheria toxin repressor-operator interactions and characterization of a mutant with decreased binding activity for divalent metals. Mol. Microbiol. 9:1993;173-181.
    • (1993) Mol. Microbiol. , vol.9 , pp. 173-181
    • Schmitt, M.P.1    Holmes, R.K.2
  • 40
    • 0028006022 scopus 로고
    • Cloning, sequence, and footprint analysis of two promotor/operators from Corynebacterium diphtheriae that are regulated by the diphtheria toxin repressor (DtxR) and Iron
    • Schmitt M. P., Holmes R. K. Cloning, sequence, and footprint analysis of two promotor/operators from Corynebacterium diphtheriae that are regulated by the diphtheria toxin repressor (DtxR) and Iron. J. Bacteriol. 176:1994;1141-1149.
    • (1994) J. Bacteriol. , vol.176 , pp. 1141-1149
    • Schmitt, M.P.1    Holmes, R.K.2
  • 41
    • 0028822995 scopus 로고
    • Characterization of an iron-dependent regulatory protein (IdeR) of Mycobacterium tuberculosis as a functional homolog of the diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae
    • Schmitt M. P., Predich M., Doukhan L., Smith I., Holmes R. K. Characterization of an iron-dependent regulatory protein (IdeR) of Mycobacterium tuberculosis as a functional homolog of the diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae. Infect. Immun. 63:1995;4284-4289.
    • (1995) Infect. Immun. , vol.63 , pp. 4284-4289
    • Schmitt, M.P.1    Predich, M.2    Doukhan, L.3    Smith, I.4    Holmes, R.K.5
  • 42
    • 0030827610 scopus 로고    scopus 로고
    • Characterization of a lipoprotein IRP1 from Corynebacterium diphtheriae, which is regulated by the diphtheria toxin repressor (DtxR) and iron
    • Schmitt M. P., Talley B. G., Holmes R. K. Characterization of a lipoprotein IRP1 from Corynebacterium diphtheriae, which is regulated by the diphtheria toxin repressor (DtxR) and iron. Infect. Immun. 65:1997;5364-5367.
    • (1997) Infect. Immun. , vol.65 , pp. 5364-5367
    • Schmitt, M.P.1    Talley, B.G.2    Holmes, R.K.3
  • 43
    • 0028184697 scopus 로고
    • Measuring the geometry of DNA grooves
    • Stofer E., Lavery R. Measuring the geometry of DNA grooves. Biopolymers. 34:1994;337-346.
    • (1994) Biopolymers , vol.34 , pp. 337-346
    • Stofer, E.1    Lavery, R.2
  • 44
    • 0026800843 scopus 로고
    • Binding of the metalloregulatory protein DtxR to the diphtheria tox operator requires a divalent heavy metal ion and protects the palindromic sequence from DNaseI digestion
    • Tao X., Murphy J. R. Binding of the metalloregulatory protein DtxR to the diphtheria tox operator requires a divalent heavy metal ion and protects the palindromic sequence from DNaseI digestion. J. Biol. Chem. 267:1992;21761-21764.
    • (1992) J. Biol. Chem. , vol.267 , pp. 21761-21764
    • Tao, X.1    Murphy, J.R.2
  • 45
    • 0027294003 scopus 로고
    • Cysteine-102 is positioned in the metal binding activation site of the Corynebacterium diphtheriae regulatory element DtxR
    • Tao X., Murphy J. R. Cysteine-102 is positioned in the metal binding activation site of the Corynebacterium diphtheriae regulatory element DtxR. Proc. Natl Acad. Sci. USA. 90:1993;8524-8528.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 8524-8528
    • Tao, X.1    Murphy, J.R.2
  • 46
    • 0000434996 scopus 로고
    • Mounting of crystals for macromolecular crystallography in a free standing thin film
    • Teng T. Y. Mounting of crystals for macromolecular crystallography in a free standing thin film. J. Appl. Crystallog. 23:1990;387-391.
    • (1990) J. Appl. Crystallog. , vol.23 , pp. 387-391
    • Teng, T.Y.1
  • 47
    • 0028267429 scopus 로고
    • Characterization of mutations that inactivate the diphtheria toxin repressor gene (DtxR)
    • Wang Z., Schmitt M. P., Holmes R. K. Characterization of mutations that inactivate the diphtheria toxin repressor gene (DtxR). Infect. Immun. 62:1994;1600-1608.
    • (1994) Infect. Immun. , vol.62 , pp. 1600-1608
    • Wang, Z.1    Schmitt, M.P.2    Holmes, R.K.3
  • 48
    • 0027402608 scopus 로고
    • The development of awareness of iron-withholding defense
    • Weinberg E. D. The development of awareness of iron-withholding defense. Prospect. Biol. Med. 36:1993;215-221.
    • (1993) Prospect. Biol. Med. , vol.36 , pp. 215-221
    • Weinberg, E.D.1
  • 49
    • 0032581662 scopus 로고    scopus 로고
    • Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex
    • White A., Ding X., van der Spek J., Murphy J. R., Ringe D. Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex. Nature. 394:1998;502-507.
    • (1998) Nature , vol.394 , pp. 502-507
    • White, A.1    Ding, X.2    Van Der Spek, J.3    Murphy, J.R.4    Ringe, D.5


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