메뉴 건너뛰기




Volumn 39, Issue 21, 2011, Pages 9433-9447

The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; GYRASE INHIBITOR; PROTEIN SUBUNIT; PROTEINASE; SIMOCYCLINONE; SIMR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 82255194409     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr640     Document Type: Article
Times cited : (55)

References (45)
  • 1
    • 19644393308 scopus 로고    scopus 로고
    • Bioactive microbial metabolites
    • Berdy, J. (2005) Bioactive microbial metabolites. J. Antibiot., 58, 1-26.
    • (2005) J. Antibiot. , vol.58 , pp. 1-26
    • Berdy, J.1
  • 5
  • 6
    • 0036219726 scopus 로고    scopus 로고
    • Simocyclinones, novel cytostatic angucyclinone antibiotics produced by Streptomyces antibioticus Tu 6040. II. Structure elucidation and biosynthesis
    • Holzenkämpfer, M., Walker, M., Zeeck, A., Schimana, J. and Fiedler, H.P. (2002) Simocyclinones, novel cytostatic angucyclinone antibiotics produced by Streptomyces antibioticus Tu 6040 II. Structure elucidation and biosynthesis. J. Antibiot., 55, 301-307. (Pubitemid 34296242)
    • (2002) Journal of Antibiotics , vol.55 , Issue.3 , pp. 301-307
    • Holzenkampfer, M.1    Walker, M.2    Zeeck, A.3    Schimana, J.4    Fiedler, H.-P.5
  • 7
    • 0033850369 scopus 로고    scopus 로고
    • Simocyclinones, novel cytostatic angucyclinone antibiotics produced by Streptomyces antibioticus Tu 6040. I. Taxonomy, fermentation, isolation and biological activities
    • Schimana, J., Fiedler, H.P., Groth, I., Süssmuth, R., Beil, W., Walker, M. and Zeeck, A. (2000) Simocyclinones, novel cytostatic angucyclinone antibiotics produced by Streptomyces antibioticus Tu 6040. I. Taxonomy, fermentation, isolation and biological activities. J. Antibiot., 53, 779-787.
    • (2000) J. Antibiot. , vol.53 , pp. 779-787
    • Schimana, J.1    Fiedler, H.P.2    Groth, I.3    Süssmuth, R.4    Beil, W.5    Walker, M.6    Zeeck, A.7
  • 8
    • 0036315519 scopus 로고    scopus 로고
    • Cloning and analysis of the simocyclinone biosynthetic gene cluster of Streptomyces antibioticus Tu 6040
    • DOI 10.1007/s00203-002-0429-z
    • Galm, U., Schimana, J., Fiedler, H.P., Schmidt, J., Li, S.M. and Heide, L. (2002) Cloning and analysis of the simocyclinone biosynthetic gene cluster of Streptomyces antibioticus Tu 6040. Arch. Microbiol., 178, 102-114. (Pubitemid 34762251)
    • (2002) Archives of Microbiology , vol.178 , Issue.2 , pp. 102-114
    • Galm, U.1    Schimana, J.2    Fiedler, H.-P.3    Schmidt, J.4    Li, S.-M.5    Heide, L.6
  • 9
    • 66949169541 scopus 로고    scopus 로고
    • Coupling of the biosynthesis and export of the DNA gyrase inhibitor simocyclinone in Streptomyces antibioticus
    • Le, T.B., Fiedler, H.P., den Hengst, C.D., Ahn, S.K., Maxwell, A. and Buttner, M.J. (2009) Coupling of the biosynthesis and export of the DNA gyrase inhibitor simocyclinone in Streptomyces antibioticus. Mol. Microbiol., 72, 1462-1474.
    • (2009) Mol. Microbiol. , vol.72 , pp. 1462-1474
    • Le, T.B.1    Fiedler, H.P.2    Den Hengst, C.D.3    Ahn, S.K.4    Maxwell, A.5    Buttner, M.J.6
  • 11
    • 0034973583 scopus 로고    scopus 로고
    • Tetracycline antibiotics: Mode of action, applications, molecular biology, and epidemiology of bacterial resistance
    • DOI 10.1128/MMBR.65.2.232-260.2001
    • Chopra, I. and Roberts, M. (2001) Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol. Mol. Biol. Rev., 65, 232-260. (Pubitemid 32538179)
    • (2001) Microbiology and Molecular Biology Reviews , vol.65 , Issue.2 , pp. 232-260
    • Chopra, I.1    Roberts, M.2
  • 13
    • 77954384737 scopus 로고    scopus 로고
    • A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators
    • Yu, Z., Reichheld, S.E., Savchenko, A., Parkinson, J. and Davidson, A.R. (2010) A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators. J. Mol. Biol., 400, 847-864.
    • (2010) J. Mol. Biol. , vol.400 , pp. 847-864
    • Yu, Z.1    Reichheld, S.E.2    Savchenko, A.3    Parkinson, J.4    Davidson, A.R.5
  • 14
    • 77957244395 scopus 로고    scopus 로고
    • Crystal structures of the multidrug binding repressor Corynebacterium glutamicum CgmR in complex with inducers and with an operator
    • Itou, H., Watanabe, N., Yao, M., Shirakihara, Y. and Tanaka, I. (2010) Crystal structures of the multidrug binding repressor Corynebacterium glutamicum CgmR in complex with inducers and with an operator. J. Mol. Biol., 403, 174-184.
    • (2010) J. Mol. Biol. , vol.403 , pp. 174-184
    • Itou, H.1    Watanabe, N.2    Yao, M.3    Shirakihara, Y.4    Tanaka, I.5
  • 15
  • 16
    • 0034087676 scopus 로고    scopus 로고
    • Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system
    • DOI 10.1038/73324
    • Orth, P., Schnappinger, D., Hillen, W., Saenger, W. and Hinrichs, W. (2000) Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat. Struct. Biol., 7, 215-219. (Pubitemid 30140767)
    • (2000) Nature Structural Biology , vol.7 , Issue.3 , pp. 215-219
    • Orth, P.1    Schnappinger, D.2    Hillen, W.3    Saenger, W.4    Hinrichs, W.5
  • 17
    • 0036500260 scopus 로고    scopus 로고
    • Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR
    • DOI 10.1093/emboj/21.5.1210
    • Schumacher, M.A., Miller, M.C., Grkovic, S., Brown, M.H., Skurray, R.A. and Brennan, R.G. (2002) Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR. EMBO J., 21, 1210-1218. (Pubitemid 34206194)
    • (2002) EMBO Journal , vol.21 , Issue.5 , pp. 1210-1218
    • Schumacher, M.A.1    Miller, M.C.2    Grkovic, S.3    Brown, M.H.4    Skurray, R.A.5    Brennan, R.G.6
  • 18
    • 79953239922 scopus 로고    scopus 로고
    • Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression
    • Le, T.B., Stevenson, C.E., Fiedler, H.P., Maxwell, A., Lawson, D.M. and Buttner, M.J. (2011) Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression. J. Mol. Biol., 408, 40-56.
    • (2011) J. Mol. Biol. , vol.408 , pp. 40-56
    • Le, T.B.1    Stevenson, C.E.2    Fiedler, H.P.3    Maxwell, A.4    Lawson, D.M.5    Buttner, M.J.6
  • 19
    • 33644874235 scopus 로고    scopus 로고
    • The integration of macromolecular diffraction data
    • Leslie, A.G. (2006) The integration of macromolecular diffraction data. Acta Crystallogr. D Biol. Crystallogr., 62, 48-57.
    • (2006) Acta Crystallogr. D Biol. Crystallogr. , vol.62 , pp. 48-57
    • Leslie, A.G.1
  • 25
    • 33646260450 scopus 로고    scopus 로고
    • Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    • Painter, J. and Merritt, E.A. (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D Biol. Crystallogr., 62, 439-450.
    • (2006) Acta Crystallogr. D Biol. Crystallogr. , vol.62 , pp. 439-450
    • Painter, J.1    Merritt, E.A.2
  • 28
    • 0018846636 scopus 로고
    • Sequencing end-labeled DNA with base-specific chemical cleavages
    • Maxam, A.M. and Gilbert, W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol., 65, 499-560.
    • (1980) Methods Enzymol. , vol.65 , pp. 499-560
    • Maxam, A.M.1    Gilbert, W.2
  • 29
    • 65449188232 scopus 로고    scopus 로고
    • Jalview version 2-a multiple sequence alignment editor and analysis workbench
    • Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. and Barton, G.J. (2009) Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
    • (2009) Bioinformatics , vol.25 , pp. 1189-1191
    • Waterhouse, A.M.1    Procter, J.B.2    Martin, D.M.3    Clamp, M.4    Barton, G.J.5
  • 30
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 31
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 32
    • 20744437001 scopus 로고    scopus 로고
    • RONN: The bio-basis function neural network technique applied to the detection of natively disordered regions in proteins
    • DOI 10.1093/bioinformatics/bti534
    • Yang, Z.R., Thomson, R., McNeil, P. and Esnouf, R.M. (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics, 21, 3369-3376. (Pubitemid 41222441)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3369-3376
    • Yang, Z.R.1    Thomson, R.2    McNeil, P.3    Esnouf, R.M.4
  • 34
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • DOI 10.1038/nrm1589
    • Dyson, H.J. and Wright, P.E. (2005) Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol., 6, 197-208. (Pubitemid 40314921)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.3 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 35
    • 0034846083 scopus 로고    scopus 로고
    • Non-hydrogen bond interactions involving the methionine sulfur atom
    • Pal, D. and Chakrabarti, P. (2001) Non-hydrogen bond interactions involving the methionine sulfur atom. J. Biomol. Struct. Dyn., 19, 115-128. (Pubitemid 32844643)
    • (2001) Journal of Biomolecular Structure and Dynamics , vol.19 , Issue.1 , pp. 115-128
    • Pal, D.1    Chakrabarti, P.2
  • 37
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253.
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5    Honig, B.6
  • 38
    • 21844452398 scopus 로고    scopus 로고
    • Characterization of the multiple transferable resistance repressor, MtrR, from Neisseria gonorrhoeae
    • DOI 10.1128/JB.187.14.5008-5012.2005
    • Hoffmann, K.M., Williams, D., Shafer, W.M. and Brennan, R.G. (2005) Characterization of the multiple transferable resistance repressor, MtrR, from Neisseria gonorrhoeae. J. Bacteriol., 187, 5008-5012. (Pubitemid 40962220)
    • (2005) Journal of Bacteriology , vol.187 , Issue.14 , pp. 5008-5012
    • Hoffmann, K.M.1    Williams, D.2    Shafer, W.M.3    Brennan, R.G.4
  • 39
    • 39149132467 scopus 로고    scopus 로고
    • Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA
    • Willems, A.R., Tahlan, K., Taguchi, T., Zhang, K., Lee, Z.Z., Ichinose, K., Junop, M.S. and Nodwell, J.R. (2008) Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA. J. Mol. Biol., 376, 1377-1387.
    • (2008) J. Mol. Biol. , vol.376 , pp. 1377-1387
    • Willems, A.R.1    Tahlan, K.2    Taguchi, T.3    Zhang, K.4    Lee, Z.Z.5    Ichinose, K.6    Junop, M.S.7    Nodwell, J.R.8
  • 40
    • 35548931586 scopus 로고    scopus 로고
    • Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure
    • DOI 10.1016/j.cell.2007.09.024, PII S0092867407012123
    • Joshi, R., Passner, J.M., Rohs, R., Jain, R., Sosinsky, A., Crickmore, M.A., Jacob, V., Aggarwal, A.K., Honig, B. and Mann, R.S. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell, 131, 530-543. (Pubitemid 350007697)
    • (2007) Cell , vol.131 , Issue.3 , pp. 530-543
    • Joshi, R.1    Passner, J.M.2    Rohs, R.3    Jain, R.4    Sosinsky, A.5    Crickmore, M.A.6    Jacob, V.7    Aggarwal, A.K.8    Honig, B.9    Mann, R.S.10
  • 41
    • 0026657433 scopus 로고
    • Refined 1.8 A crystal structure of the lambda repressor-operator complex
    • Beamer, L.J. and Pabo, C.O. (1992) Refined 1.8 A crystal structure of the lambda repressor-operator complex. J. Mol. Biol., 227, 177-196.
    • (1992) J. Mol. Biol. , vol.227 , pp. 177-196
    • Beamer, L.J.1    Pabo, C.O.2
  • 42
    • 0032522139 scopus 로고    scopus 로고
    • DNA bending: The prevalence of kinkiness and the virtues of normality
    • DOI 10.1093/nar/26.8.1906
    • Dickerson, R.E. (1998) DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res., 26, 1906-1926. (Pubitemid 28291723)
    • (1998) Nucleic Acids Research , vol.26 , Issue.8 , pp. 1906-1926
    • Dickerson, R.E.1
  • 43
    • 33646195686 scopus 로고    scopus 로고
    • Detection of protein assemblies in crystals
    • Berthold, M.R., Glen, R.C., Diederichs, K., Kohlbacher, O. and Fischer, I. (eds) Springer-Verlag, Berlin Heidelberg
    • Krissinel, E. and Henrick, K. (2005) Detection of protein assemblies in crystals. In Berthold, M.R., Glen, R.C., Diederichs, K., Kohlbacher, O. and Fischer, I. (eds), Computational Life Sciences, Vol. 3695. Springer-Verlag, Berlin Heidelberg, pp. 163-174.
    • (2005) Computational Life Sciences , vol.3695 , pp. 163-174
    • Krissinel, E.1    Henrick, K.2
  • 44
    • 76049113822 scopus 로고    scopus 로고
    • The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor
    • Reichheld, S.E., Yu, Z. and Davidson, A.R. (2009) The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor. Proc. Natl Acad. Sci. USA, 106, 22263-22268.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 22263-22268
    • Reichheld, S.E.1    Yu, Z.2    Davidson, A.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.