-
1
-
-
79958166755
-
TetR family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation
-
Agari Y, Agari K, Sakamoto K, Kuramitsu S, Shinkai A. 2011. TetR family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation. Microbiology 157:1589-1601.
-
(2011)
Microbiology
, vol.157
, pp. 1589-1601
-
-
Agari, Y.1
Agari, K.2
Sakamoto, K.3
Kuramitsu, S.4
Shinkai, A.5
-
2
-
-
51649108915
-
Global gene expression mediated by Thermus thermophilus SdrP, a CRP/ FNR family transcriptional regulator
-
Agari Y, Kashihara A, Yokoyama S, Kuramitsu S, Shinkai A. 2008. Global gene expression mediated by Thermus thermophilus SdrP, a CRP/ FNR family transcriptional regulator. Mol. Microbiol. 70:60-75.
-
(2008)
Mol. Microbiol.
, vol.70
, pp. 60-75
-
-
Agari, Y.1
Kashihara, A.2
Yokoyama, S.3
Kuramitsu, S.4
Shinkai, A.5
-
3
-
-
0035964342
-
Electrostatics of nanosystems: application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U. S. A. 98:10037-10041.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
Mccammon, J.A.5
-
4
-
-
3543012707
-
Crystallography and NMR system: A new software suite for macromolecular structure determination
-
Brünger AT, et al. 1998. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54:905-921.
-
(1998)
Acta Crystallogr. D Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brünger, A.T.1
-
5
-
-
0028103275
-
The CCP4 suite: programs for protein crystallography
-
Collaborative Computational Project Number 4.
-
Collaborative Computational Project Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50:760-763.
-
(1994)
Acta Crystallogr. D Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
-
8
-
-
0043123208
-
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins
-
Gouet P, Robert X, Courcelle E. 2003. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31:3320-3323.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3320-3323
-
-
Gouet, P.1
Robert, X.2
Courcelle, E.3
-
9
-
-
0032541162
-
QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA
-
Grkovic S, Brown MH, Roberts NJ, Paulsen IT, Skurray RA. 1998. QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. J. Biol. Chem. 273:18665-18673.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 18665-18673
-
-
Grkovic, S.1
Brown, M.H.2
Roberts, N.J.3
Paulsen, I.T.4
Skurray, R.A.5
-
10
-
-
0035205399
-
The staphylococcal QacR multidrug regulator binds a correctly spaced operator as a pair of dimers
-
Grkovic S, Brown MH, Schumacher MA, Brennan RG, Skurray RA. 2001. The staphylococcal QacR multidrug regulator binds a correctly spaced operator as a pair of dimers. J. Bacteriol. 183:7102-7109.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 7102-7109
-
-
Grkovic, S.1
Brown, M.H.2
Schumacher, M.A.3
Brennan, R.G.4
Skurray, R.A.5
-
11
-
-
0035850879
-
Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker
-
Hashimoto Y, Yano T, Kuramitsu S, Kagamiyama H. 2001. Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett. 506:231-234.
-
(2001)
FEBS Lett.
, vol.506
, pp. 231-234
-
-
Hashimoto, Y.1
Yano, T.2
Kuramitsu, S.3
Kagamiyama, H.4
-
12
-
-
0028244325
-
Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance
-
Hinrichs W, et al. 1994. Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance. Science 264:418-420.
-
(1994)
Science
, vol.264
, pp. 418-420
-
-
Hinrichs, W.1
-
13
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
14
-
-
0028952251
-
The complex formed between Tet repressor and tetracycline-Mg2Universal-GreekwithMathPi-1
-
Kisker C, Hinrichs W, Tovar K, Hillen W, Saenger W. 1995. The complex formed between Tet repressor and tetracycline-Mg2Universal-GreekwithMathPi.-1.H11001 reveals mechanism of antibiotic resistance. J. Mol. Biol. 247:260-280.
-
(1995)
H11001 reveals mechanism of antibiotic resistance. J. Mol. Biol.
, vol.247
, pp. 260-280
-
-
Kisker, C.1
Hinrichs, W.2
Tovar, K.3
Hillen, W.4
Saenger, W.5
-
15
-
-
0025366034
-
Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity
-
Kuramitsu S, Hiromi K, Hayashi H, Morino Y, Kagamiyama H. 1990. Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity. Biochemistry 29:5469-5476.
-
(1990)
Biochemistry
, vol.29
, pp. 5469-5476
-
-
Kuramitsu, S.1
Hiromi, K.2
Hayashi, H.3
Morino, Y.4
Kagamiyama, H.5
-
16
-
-
36448991500
-
Clustal W and Clustal X version 2
-
Larkin MA, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
-
(2007)
0. Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
-
17
-
-
82255194409
-
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
-
Le TB, Schumacher MA, Lawson DM, Brennan RG, Buttner MJ. 2011. 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. Nucleic Acids Res. 39:9433-9447.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 9433-9447
-
-
Le, T.B.1
Schumacher, M.A.2
Lawson, D.M.3
Brennan, R.G.4
Buttner, M.J.5
-
18
-
-
79953239922
-
Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression
-
Le TB, et al. 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
-
19
-
-
0022273106
-
1H-15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type
-
LeMaster DM, Richards FM. 1985. 1H-15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry 24:7263-7268.
-
(1985)
Biochemistry
, vol.24
, pp. 7263-7268
-
-
Lemaster, D.M.1
Richards, F.M.2
-
20
-
-
0035057115
-
The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications
-
Luengo JM, Garcia JL, Olivera ER. 2001. The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications. Mol. Microbiol. 39:1434-1442.
-
(2001)
Mol. Microbiol.
, vol.39
, pp. 1434-1442
-
-
Luengo, J.M.1
Garcia, J.L.2
Olivera, E.R.3
-
21
-
-
0036087630
-
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
-
Marchler-Bauer A, et al. 2002. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30:281-283.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 281-283
-
-
Marchler-Bauer, A.1
-
22
-
-
77950656400
-
A novel role of malonyl-ACP in lipid homeostasis
-
Martinez MA, et al. 2010. A novel role of malonyl-ACP in lipid homeostasis. Biochemistry 49:3161-3167.
-
(2010)
Biochemistry
, vol.49
, pp. 3161-3167
-
-
Martinez, M.A.1
-
23
-
-
33646596266
-
Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea
-
Minezaki Y, Homma K, Nishikawa K. 2005. Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea. DNA Res. 12:269-280.
-
(2005)
DNA Res.
, vol.12
, pp. 269-280
-
-
Minezaki, Y.1
Homma, K.2
Nishikawa, K.3
-
24
-
-
84857914339
-
The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination
-
Ohtani N, Tomita M, Itaya M. 2012. The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination. Extremophiles 16:237-244.
-
(2012)
Extremophiles
, vol.16
, pp. 237-244
-
-
Ohtani, N.1
Tomita, M.2
Itaya, M.3
-
25
-
-
0032486128
-
Conformational changes of the Tet repressor induced by tetracycline trapping
-
Orth P, et al. 1998. Conformational changes of the Tet repressor induced by tetracycline trapping. J. Mol. Biol. 279:439-447.
-
(1998)
J. Mol. Biol.
, vol.279
, pp. 439-447
-
-
Orth, P.1
-
26
-
-
0034087676
-
Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system.
-
Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs W. 2000. Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat. Struct. Biol. 7:215-219.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 215-219
-
-
Orth, P.1
Schnappinger, D.2
Hillen, W.3
Saenger, W.4
Hinrichs, W.5
-
28
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326.
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
29
-
-
34548092055
-
The utility of MAS5 expression summary and detection call algorithms
-
Pepper SD, Saunders EK, Edwards LE, Wilson CL, Miller CJ. 2007. The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics 8:273.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 273
-
-
Pepper, S.D.1
Saunders, E.K.2
Edwards, L.E.3
Wilson, C.L.4
Miller, C.J.5
-
30
-
-
20544432535
-
The TetR family of transcriptional repressors
-
Ramos JL, et al. 2005. The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69:326-356.
-
(2005)
Microbiol. Mol. Biol. Rev.
, vol.69
, pp. 326-356
-
-
Ramos, J.L.1
-
31
-
-
76049113822
-
The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor
-
Reichheld SE, Yu Z, Davidson AR. 2009. The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor. Proc. Natl. Acad. Sci. U. S. A. 106:22263-22268.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 22263-22268
-
-
Reichheld, S.E.1
Yu, Z.2
Davidson, A.R.3
-
32
-
-
34548219522
-
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
-
Rodionov DA. 2007. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem. Rev. 107:3467-3497.
-
(2007)
Chem. Rev.
, vol.107
, pp. 3467-3497
-
-
Rodionov, D.A.1
-
33
-
-
80052322974
-
Phenylacetyl coenzyme A is an effector molecule of the TetR family transcriptional repressor PaaR from Thermus thermophilus HB8
-
Sakamoto K, Agari Y, Kuramitsu S, Shinkai A. 2011. Phenylacetyl coenzyme A is an effector molecule of the TetR family transcriptional repressor PaaR from Thermus thermophilus HB8. J. Bacteriol. 193:4388-4395.
-
(2011)
J. Bacteriol.
, vol.193
, pp. 4388-4395
-
-
Sakamoto, K.1
Agari, Y.2
Kuramitsu, S.3
Shinkai, A.4
-
34
-
-
0036500260
-
Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR
-
Schumacher MA, et al. 2002. Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR. EMBO J. 21: 1210-1218.
-
(2002)
EMBO J.
, vol.21
, pp. 1210-1218
-
-
Schumacher, M.A.1
-
35
-
-
0035824388
-
Structural mechanisms of QacR induction and multidrug recognition
-
Schumacher MA, et al. 2001. Structural mechanisms of QacR induction and multidrug recognition. Science 294:2158-2163.
-
(2001)
Science
, vol.294
, pp. 2158-2163
-
-
Schumacher, M.A.1
-
36
-
-
34248359835
-
Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8
-
Shinkai A, et al. 2007. Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J. Bacteriol. 189:3891-3901.
-
(2007)
J. Bacteriol.
, vol.189
, pp. 3891-3901
-
-
Shinkai, A.1
-
39
-
-
77956292377
-
Bacterial phenylalanine and phenylacetate catabolic pathway revealed
-
Teufel R, et al. 2010. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. U. S. A. 107:14390-14395.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 14390-14395
-
-
Teufel, R.1
-
40
-
-
33747670167
-
RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation
-
Ueno G, et al. 2006. RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation. J. Struct. Funct. Genomics 7:15-22.
-
(2006)
J. Struct. Funct. Genomics
, vol.7
, pp. 15-22
-
-
Ueno, G.1
-
41
-
-
39149132467
-
Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA
-
Willems AR, et al. 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
-
42
-
-
77954384737
-
A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators
-
Yu Z, Reichheld SE, Savchenko A, Parkinson J, Davidson AR. 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
|