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Volumn 342, Issue 4, 2004, Pages 1155-1169

Crystal structure of an IdeR-DNA complex reveals a conformational change in activated IdeR for base-specific interactions

Author keywords

IdeR; iron acquisition; iron dependent regulator; Mycobacterium tuberculosis; siderophores

Indexed keywords

ASPARTIC ACID; COBALT; DNA; DOUBLE STRANDED DNA; HELIX LOOP HELIX PROTEIN; PROTEIN SUBUNIT; SODIUM; THYMINE;

EID: 4444371630     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.07.083     Document Type: Article
Times cited : (57)

References (43)
  • 2
    • 0033581124 scopus 로고    scopus 로고
    • Consensus statement. Global burden of tuberculosis: Estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project
    • C. Dye, S. Scheele, P. Dolin, V. Parthania, and M.C. Raviglione Consensus statement. Global burden of tuberculosis: estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project J. Am. Med. Assoc. 282 1999 677 686
    • (1999) J. Am. Med. Assoc. , vol.282 , pp. 677-686
    • Dye, C.1    Scheele, S.2    Dolin, P.3    Parthania, V.4    Raviglione, M.C.5
  • 4
    • 0038182170 scopus 로고    scopus 로고
    • Tuberculosis trends in the United States, 1992-2001
    • E. Schneider, and K.G. Castro Tuberculosis trends in the United States, 1992-2001 Tuberculosis 83 2003 21 29
    • (2003) Tuberculosis , vol.83 , pp. 21-29
    • Schneider, E.1    Castro, K.G.2
  • 5
    • 0030796825 scopus 로고    scopus 로고
    • Assessment of worldwide tuberculosis control. WHO Global Surveillance and Monitoring Project
    • M.C. Raviglione, C. Dye, S. Schmidt, and A. Kochi Assessment of worldwide tuberculosis control. WHO Global Surveillance and Monitoring Project Lancet 350 1997 624 629
    • (1997) Lancet , vol.350 , pp. 624-629
    • Raviglione, M.C.1    Dye, C.2    Schmidt, S.3    Kochi, A.4
  • 6
    • 0028889845 scopus 로고
    • Global epidemiology of tuberculosis. Morbidity and mortality of a worldwide epidemic
    • M.C. Raviglione, D.E.J. Snider, and A. Kochi Global epidemiology of tuberculosis. Morbidity and mortality of a worldwide epidemic J. Am. Med. Assoc. 273 1995 220 226
    • (1995) J. Am. Med. Assoc. , vol.273 , pp. 220-226
    • Raviglione, M.C.1    Snider, D.E.J.2    Kochi, A.3
  • 7
    • 0001590980 scopus 로고    scopus 로고
    • Crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied
    • E. Pohl, R.K. Holmes, and W.G. Hol 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.3
  • 8
    • 0035937172 scopus 로고    scopus 로고
    • Crystal structure of the iron-dependent regulator from Mycobacterium tuberculosis at 2.0-Å resolution reveals the Src homology domain 3-like fold and metal binding function of the third domain
    • M.D. Feese, B.P. Ingason, J. Goranson-Siekierke, R.K. Holmes, and W.G. Hol Crystal structure of the iron-dependent regulator from Mycobacterium tuberculosis at 2.0-Å resolution reveals the Src homology domain 3-like fold and metal binding function of the third domain J. Biol. Chem. 276 2001 5959 5966
    • (2001) J. Biol. Chem. , vol.276 , pp. 5959-5966
    • Feese, M.D.1    Ingason, B.P.2    Goranson-Siekierke, J.3    Holmes, R.K.4    Hol, W.G.5
  • 9
    • 0033759220 scopus 로고    scopus 로고
    • Iron metabolism in pathogenic bacteria
    • C. Ratledge, and L.G. Dover Iron metabolism in pathogenic bacteria Annu. Rev. Microbiol. 54 2000 881 941
    • (2000) Annu. Rev. Microbiol. , vol.54 , pp. 881-941
    • Ratledge, C.1    Dover, L.G.2
  • 10
    • 0014803645 scopus 로고
    • Mycobactins: Iron-chelating growth factors from mycobacteria
    • G.A. Snow Mycobactins: iron-chelating growth factors from mycobacteria Bacteriol. Rev. 34 1970 99 125
    • (1970) Bacteriol. Rev. , vol.34 , pp. 99-125
    • Snow, G.A.1
  • 11
    • 0028999977 scopus 로고
    • Iron acquisition by Mycobacterium tuberculosis: Isolation and characterization of a family of iron-binding exochelins
    • J. Gobin, C.H. Moore, J.R.J. Reeve, D.K. Wong, B.W. Gibson, and M.A. Horwitz Iron acquisition by Mycobacterium tuberculosis: isolation and characterization of a family of iron-binding exochelins Proc. Natl Acad. Sci. USA 92 1995 5189 5193
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 5189-5193
    • Gobin, J.1    Moore, C.H.2    Reeve, J.R.J.3    Wong, D.K.4    Gibson, B.W.5    Horwitz, M.A.6
  • 12
    • 0034307852 scopus 로고    scopus 로고
    • The iron dependent regulatory protein IdeR (DtxR) of Rhodococcus equi
    • C.A. Boland, and W.G. Meijer The iron dependent regulatory protein IdeR (DtxR) of Rhodococcus equi FEMS Microbiol. Letters 191 2000 1 5
    • (2000) FEMS Microbiol. Letters , vol.191 , pp. 1-5
    • Boland, C.A.1    Meijer, W.G.2
  • 13
    • 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
    • M.P. Schmitt, M. Predich, L. Doukhan, I. Smith, and R.K. Holmes 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. 11 1995 4284 4289
    • (1995) Infect. Immun. , vol.11 , pp. 4284-4289
    • Schmitt, M.P.1    Predich, M.2    Doukhan, L.3    Smith, I.4    Holmes, R.K.5
  • 14
    • 0036081140 scopus 로고    scopus 로고
    • IdeR, an essential gene in Mycobacterium tuberculosis: Role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response
    • G.M. Rodriquez, M.T. Voskuil, B. Gold, G.K. Schoolnik, and I. Smith IdeR, an essential gene in Mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response Infect. Immun. 70 2002 3371 3381
    • (2002) Infect. Immun. , vol.70 , pp. 3371-3381
    • Rodriquez, G.M.1    Voskuil, M.T.2    Gold, B.3    Schoolnik, G.K.4    Smith, I.5
  • 15
    • 0033000384 scopus 로고    scopus 로고
    • Transcriptional control of the iron-responsive fxbA gene by the mycobacterial regulator IdeR
    • O. Dussurget, J. Timm, M. Gomez, B. Gold, S. Yu, and S.Z. Sabol Transcriptional control of the iron-responsive fxbA gene by the mycobacterial regulator IdeR J. Bacteriol. 181 1999 3402 3408
    • (1999) J. Bacteriol. , vol.181 , pp. 3402-3408
    • Dussurget, O.1    Timm, J.2    Gomez, M.3    Gold, B.4    Yu, S.5    Sabol, S.Z.6
  • 16
    • 0032833150 scopus 로고    scopus 로고
    • Identification and characterization of two divergently transcribed iron regulated genes in Mycobacterium tuberculosis
    • G.M. Rodriquez, B.M.G. Gold, O. Dussurget, and I. Smith Identification and characterization of two divergently transcribed iron regulated genes in Mycobacterium tuberculosis Tuber. Lung Dis. 79 1999 287 298
    • (1999) Tuber. Lung Dis. , vol.79 , pp. 287-298
    • Rodriquez, G.M.1    Gold, B.M.G.2    Dussurget, O.3    Smith, I.4
  • 17
    • 0035169902 scopus 로고    scopus 로고
    • The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages
    • B. Gold, G.M. Rodriquez, S.A. Marras, M. Petecost, and I. Smith The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages Mol. Microbiol. 42 2001 851 865
    • (2001) Mol. Microbiol. , vol.42 , pp. 851-865
    • Gold, B.1    Rodriquez, G.M.2    Marras, S.A.3    Petecost, M.4    Smith, I.5
  • 18
    • 0032211974 scopus 로고    scopus 로고
    • Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin
    • L.E. Quadri, J. Sello, T.A. Keating, P.H. Weinreb, and C.T. Walsh Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin Chem. Biol. 5 1998 631 645
    • (1998) Chem. Biol. , vol.5 , pp. 631-645
    • Quadri, L.E.1    Sello, J.2    Keating, T.A.3    Weinreb, P.H.4    Walsh, C.T.5
  • 19
    • 0003116644 scopus 로고    scopus 로고
    • Iron-dependent regulators
    • K. Wieghardt R. Huber T.L. Poulos A. Messerschmidt Jon Wiley & Sons Chichester
    • M.D. Feese, W.G. Hol, E. Pohl, and R.K. Holmes Iron-dependent regulators K. Wieghardt R. Huber T.L. Poulos A. Messerschmidt Handbook of Metalloproteins 2001 Jon Wiley & Sons Chichester
    • (2001) Handbook of Metalloproteins
    • Feese, M.D.1    Hol, W.G.2    Pohl, E.3    Holmes, R.K.4
  • 20
    • 0032581662 scopus 로고    scopus 로고
    • Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex
    • A. White, X. Ding, J.C. vanderSpek, J.R. Murphy, and D. Ringe Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex Nature 394 1998 502 506
    • (1998) Nature , vol.394 , pp. 502-506
    • White, A.1    Ding, X.2    Vanderspek, J.C.3    Murphy, J.R.4    Ringe, D.5
  • 21
    • 0000868851 scopus 로고    scopus 로고
    • Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain
    • E. Pohl, R.K. Holmes, and W.G. Hol Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain J. Mol. Biol. 292 1999 653 667
    • (1999) J. Mol. Biol. , vol.292 , pp. 653-667
    • Pohl, E.1    Holmes, R.K.2    Hol, W.G.3
  • 22
    • 0034730114 scopus 로고    scopus 로고
    • Methyl groups of thymine bases are important for nucleic acid recognition by DtxR
    • C.S. Chen, A. White, J. Love, J.R. Murphy, and D. Ringe Methyl groups of thymine bases are important for nucleic acid recognition by DtxR Biochemistry 39 2000 10397 10407
    • (2000) Biochemistry , vol.39 , pp. 10397-10407
    • Chen, C.S.1    White, A.2    Love, J.3    Murphy, J.R.4    Ringe, D.5
  • 23
    • 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
    • X. Qiu, E. Pohl, R.K. Holmes, and W.G. Hol 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.4
  • 24
    • 0028826149 scopus 로고
    • Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae
    • N. Schiering, X. Tao, H. Zeng, J.R. Murphy, G.A. Petsko, and D. Ringe 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
  • 25
    • 0028993911 scopus 로고
    • Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors
    • X. Qiu, C. Verlinde, S. Zhang, M. Schmitt, R. Holmes, and W. Hol Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors Structure 3 1995 87 100
    • (1995) Structure , vol.3 , pp. 87-100
    • Qiu, X.1    Verlinde, C.2    Zhang, S.3    Schmitt, M.4    Holmes, R.5    Hol, W.6
  • 26
    • 0032575642 scopus 로고    scopus 로고
    • Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR
    • E. Pohl, R.K. Holmes, and W.G. Hol Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR J. Biol. Chem. 273 1998 22420 22427
    • (1998) J. Biol. Chem. , vol.273 , pp. 22420-22427
    • Pohl, E.1    Holmes, R.K.2    Hol, W.G.3
  • 27
    • 0033179802 scopus 로고    scopus 로고
    • The geometry of metal-ligand interactions relevant to proteins
    • M.M. Harding The geometry of metal-ligand interactions relevant to proteins Acta Crystallog. sect. D 55 1999 1432 1443
    • (1999) Acta Crystallog. Sect. D , vol.55 , pp. 1432-1443
    • Harding, M.M.1
  • 28
    • 0035094475 scopus 로고    scopus 로고
    • Geometry of metal-ligand interactions in proteins
    • M.M. Harding Geometry of metal-ligand interactions in proteins Acta Crystallog. sect. D 57 2001 401 411
    • (2001) Acta Crystallog. Sect. D , vol.57 , pp. 401-411
    • Harding, M.M.1
  • 29
    • 0036014793 scopus 로고    scopus 로고
    • Metal-ligand geometry relevant to proteins and in proteins: Sodium and potassium
    • M.M. Harding Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium Acta Crystallog. sect. D 58 2002 872 874
    • (2002) Acta Crystallog. Sect. D , vol.58 , pp. 872-874
    • Harding, M.M.1
  • 30
    • 0346665686 scopus 로고    scopus 로고
    • Is the bond-valence method able to identify metal atoms in protein structures?
    • P. Muller, S. Kopke, and G.M. Sheldrick Is the bond-valence method able to identify metal atoms in protein structures? Acta Crystallog. sect. D 59 2003 32 37
    • (2003) Acta Crystallog. Sect. D , vol.59 , pp. 32-37
    • Muller, P.1    Kopke, S.2    Sheldrick, G.M.3
  • 31
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • R. Lavery, and H. Sklenar The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids J. Biomol. Struct. Dynam. 6 1988 63 91
    • (1988) J. Biomol. Struct. Dynam. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 32
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • R. Lavery, and H. Sklenar Defining the structure of irregular nucleic acids: conventions and principles J. Biomol. Struct. Dynam. 6 1989 655 667
    • (1989) J. Biomol. Struct. Dynam. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 33
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • (Carter, C. W. J. & Sweet, R. M., eds), Academic Press, New York.
    • Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology (Carter, C. W. J. & Sweet, R. M., eds), vol. 276, pp 307-326, Academic Press, New York.
    • (1997) Methods in Enzymology , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 34
    • 0000952473 scopus 로고
    • On the treatment of negative intensity observations
    • A. French, and K. Wilson On the treatment of negative intensity observations Acta Crystallog. sect. A 34 1978 517 525
    • (1978) Acta Crystallog. Sect. A , vol.34 , pp. 517-525
    • French, A.1    Wilson, K.2
  • 35
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallog. 30 1997 1022 1025
    • (1997) J. Appl. Crystallog. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 36
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • B.W. Matthews 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
  • 37
    • 0034517589 scopus 로고    scopus 로고
    • An approach to multi-copy search in molecular replacement
    • A. Vagin, and A. Teplyakov An approach to multi-copy search in molecular replacement Acta Crystallog. sect. D 56 2000 1622 1624
    • (2000) Acta Crystallog. Sect. D , vol.56 , pp. 1622-1624
    • Vagin, A.1    Teplyakov, A.2
  • 38
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallog. sect. D 53 1997 240 255
    • (1997) Acta Crystallog. Sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 40
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit - A versatile program for manipulating atomic coordinates and electron density
    • D.E. McRee XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
    • (1999) J. Struct. Biol. , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 41
    • 0031574026 scopus 로고    scopus 로고
    • NUCPLOT: A program to generate schematic diagrams of protein-nucleic acid interactions
    • N.M. Luscombe, R.A. Laskowski, and J.M. Thornton NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions Nucl. Acids Res. 25 1997 4940 4945
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4940-4945
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 42
    • 0344825084 scopus 로고    scopus 로고
    • Analysis of the Corynebacterium diphtheriae DtxR regulon: Identification of a putative siderophore synthesis and transport system that is similar to the Yersinia high-pathogenicity island-encoded yersiniabactin synthesis and uptake system
    • C.A. Kunkle, and M.P. Schmitt Analysis of the Corynebacterium diphtheriae DtxR regulon: identification of a putative siderophore synthesis and transport system that is similar to the Yersinia high-pathogenicity island-encoded yersiniabactin synthesis and uptake system J. Bacteriol. 185 2003 6826 6840
    • (2003) J. Bacteriol. , vol.185 , pp. 6826-6840
    • Kunkle, C.A.1    Schmitt, M.P.2
  • 43
    • 2942525902 scopus 로고    scopus 로고
    • Characterization of the iron-regulated desA promoter of Streptomyces pilosus as a system for controlled gene expression in actinomycetes
    • F.J. Flores, J. Rincon, and J.F. Martin Characterization of the iron-regulated desA promoter of Streptomyces pilosus as a system for controlled gene expression in actinomycetes Microb. Cell Fact. 2 2003 5
    • (2003) Microb. Cell Fact. , vol.2 , pp. 5
    • Flores, F.J.1    Rincon, J.2    Martin, J.F.3


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