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of outstanding interest. This paper presents crystal structures of the intact tetrameric apo lac repressor and complexes with 21-base-pair symmetric operators and the gratuitous inducer IPTG. The DNA complex shows binding of the N-terminal HTH motif to the major groove and a pair of hinge helices binding to the minor groove, which causes severe bending of the DNA similar to that seen in the dimeric PurP complexed to DNA. The three forms differ in the relative orientation of the subdomains of the core. From the three structures, a model for allostery and looping is proposed.
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Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. of outstanding interest Science. 271:1996;1247-1254 This paper presents crystal structures of the intact tetrameric apo lac repressor and complexes with 21-base-pair symmetric operators and the gratuitous inducer IPTG. The DNA complex shows binding of the N-terminal HTH motif to the major groove and a pair of hinge helices binding to the minor groove, which causes severe bending of the DNA similar to that seen in the dimeric PurP complexed to DNA. The three forms differ in the relative orientation of the subdomains of the core. From the three structures, a model for allostery and looping is proposed.
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Lewis, M.1
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Slijper M, Bonvin AMJJ, Boelens R, Kaptein R. Refined structure of the lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator. of outstanding interest J Mol Biol. 259:1996;761-773 See annotation [7].
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Slijper, M.1
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of outstanding interest. This paper, together with [6], describes the refined structure for the headpiece fragment (residues 1 -56) of the lac repressor determined using NMR spectroscopy. A comparison of this structure with the DNA-complexed lac repressor fragment in solution shows that a loop region between the recognition helix and the following helix significantly changes conformation upon DNA binding.
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Kaptein R, Slijper M, Boelens R. Structure and dynamics of the lac repressor-operator complex as determined by NMR. of outstanding interest Toxicol Lett. 82/83:1996;591-599 This paper, together with [6], describes the refined structure for the headpiece fragment (residues 1 -56) of the lac repressor determined using NMR spectroscopy. A comparison of this structure with the DNA-complexed lac repressor fragment in solution shows that a loop region between the recognition helix and the following helix significantly changes conformation upon DNA binding.
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Kaptein, R.1
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Ellenberger TE, Brandl CJ, Struhl K, Harrison SC. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α helices: crystal structure of the protein-DNA complex. Cell. 71:1992;1223-1237.
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Ellenberger, T.E.1
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Oh B-H, Ames GF-L, Kim S-H. Structural basis for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein. J Biol Chem. 269:1994;26323-26330.
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Mechanisms of corepressor-mediated specific DNA binding by purine repressor
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of special interest. The authors report the crystal structure of a truncated form of PurR in which the N-terminal hinge helices and HTH domains are missing. A comparison of this core structure to the intact PurR - hypoxanthine - DNA complex [8] shows that the ligand binding pocket is restructured and relative orientation of the subdomains of the ligand binding domain changes.
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Schumacher MA, Choi KY, Lu F, Zalkin H, Brennan RG. Mechanisms of corepressor-mediated specific DNA binding by purine repressor. of special interest Cell. 83:1995;147-155 The authors report the crystal structure of a truncated form of PurR in which the N-terminal hinge helices and HTH domains are missing. A comparison of this core structure to the intact PurR - hypoxanthine - DNA complex [8] shows that the ligand binding pocket is restructured and relative orientation of the subdomains of the ligand binding domain changes.
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Cell
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Schumacher, M.A.1
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Lu, F.3
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Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex
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of special interest. This paper describes the use of modified nucleotides, substituted at either single sites or at complementary base pairs, to examine direct and indirect influences on the stability of lac repressor - operator interactions.
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Zhang X, Gottlieb PA. Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex. of special interest Nucleic Acids Res. 23:1995;1502-1511 This paper describes the use of modified nucleotides, substituted at either single sites or at complementary base pairs, to examine direct and indirect influences on the stability of lac repressor - operator interactions.
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Nucleic Acids Res
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Zhang, X.1
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V. Allfrey, V. Bautz, E.K.F. McCarthy, R.T. Schirnke, Tissieres A. Berlin: Abakon Verlagsgesellschaft
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Gilbert, W.1
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31
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3 are separated by 92 base pairs.
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3 are separated by 92 base pairs.
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J Mol Biol
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Müller, J.1
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Müller-Hill, B.3
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32
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0030564945
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sym operators to a Lacl tetramer: Evidence for contributions of non-operator DNA binding by wrapping and looping
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of special interest. The authors thoroughly examine lac repressor¥mmetric operator interactions over a range of protein, DNA and salt concentrations. The repressor tetramer was found to be more stable than previously thought. At high salt concentrations, binding of the repressor to symmetric operator sites on a plasmid is noncooperative. At lower salt concentrations, anticooperativity of binding a second operator site increases. The authors propose that nonspecific binding and DNA looping at low salt may cause stabilization of the 1:1 lac repressor: operator complex.
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sym operators to a Lacl tetramer: evidence for contributions of non-operator DNA binding by wrapping and looping. of special interest J Mol Biol. 260:1996;697-717 The authors thoroughly examine lac repressor¥mmetric operator interactions over a range of protein, DNA and salt concentrations. The repressor tetramer was found to be more stable than previously thought. At high salt concentrations, binding of the repressor to symmetric operator sites on a plasmid is noncooperative. At lower salt concentrations, anticooperativity of binding a second operator site increases. The authors propose that nonspecific binding and DNA looping at low salt may cause stabilization of the 1:1 lac repressor: operator complex.
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J Mol Biol
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Levandoski, M.M.1
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Record, M.T.6
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33
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0029927848
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The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter
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of special interest. The authors describe measurements of the cooperativity between lac repressor and catabolite activating protein (CAP) at their primary binding sites in the lac promoter. Mechanisms for cooperativity are discussed. A mechanism that involves looping is suggested.
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Vossen KM, Stickle DF, Fried MG. The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter. of special interest J Mol Biol. 255:1996;44-54 The authors describe measurements of the cooperativity between lac repressor and catabolite activating protein (CAP) at their primary binding sites in the lac promoter. Mechanisms for cooperativity are discussed. A mechanism that involves looping is suggested.
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J Mol Biol
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Vossen, K.M.1
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Fried, M.G.3
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34
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Transcription regulation by inflexibility of promoter DNA in a looped complex
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of special interest. See annotation [35].
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Choy HE, Park S-W, Parrack P, Adhya S. Transcription regulation by inflexibility of promoter DNA in a looped complex. of special interest Proc Natl Acad Sci USA. 92:1995;7327-7331 See annotation [35].
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Proc Natl Acad Sci USA
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Choy, H.E.1
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Adhya, S.4
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35
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0029153579
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Repression and activation of transcription by Gal and Lac repressors: Involvement of alpha subunit of RNA polymerase
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of special interest. This paper together with [34] discusses DNA looping involved in the lac and gal operon systems.
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Choy HE, Park SW, Aki T, Parrack P, Fujita N, Ishihama A, Adhya S. Repression and activation of transcription by Gal and Lac repressors: involvement of alpha subunit of RNA polymerase. of special interest EMBO J. 14:1995;4523-4529 This paper together with [34] discusses DNA looping involved in the lac and gal operon systems.
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EMBO J
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Choy, H.E.1
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Ishihama, A.6
Adhya, S.7
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36
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0028956979
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Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules
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of special interest. This paper describes the detection of DNA looping by the lac repressor using Brownian motion of microscopic particles that are chemically attached to the ends of the DNA molecules. Rates for loop formation and breakdown are discussed.
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Finzi L, Gelles J. Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. of special interest Science. 267:1995;378-380 This paper describes the detection of DNA looping by the lac repressor using Brownian motion of microscopic particles that are chemically attached to the ends of the DNA molecules. Rates for loop formation and breakdown are discussed.
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(1995)
Science
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Finzi, L.1
Gelles, J.2
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Interaction of affecting ligands with lac repressor and repressor-operator complex
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Barkley MD, Riggs AD, Jobe A, Bourgeois S. Interaction of affecting ligands with lac repressor and repressor-operator complex. Biochemistry. 14:1975;1700-1712.
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Biochemistry
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0028845578
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Mechanism of lac repressor switch-off: Orientation of the lac repressor DNA-binding domain is reversed upon inducer binding
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of special interest. See annotation [40].
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Kamashev DE, Esipova NG, Ebralidse KK, Mirzabekov AD. Mechanism of lac repressor switch-off: orientation of the lac repressor DNA-binding domain is reversed upon inducer binding. of special interest FEBS Lett. 375:1995;27-30 See annotation [40].
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FEBS Lett
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Kamashev, D.E.1
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Mirzabekov, A.D.4
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40
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21844502301
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Effect of inducer on the lac repressor headpiece orientation
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of special interest. This paper together with [39] describes protein - DNA cross linking experiments for the lac repressor. The authors suggest that the presence of inducer causes the HTH motifs to reverse their orientation.
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Kamashev D, Ebralidze K, Esipova NG, Mirzabekov AD. Effect of inducer on the lac repressor headpiece orientation. of special interest Mol Biol. 29:1995;553-560 This paper together with [39] describes protein - DNA cross linking experiments for the lac repressor. The authors suggest that the presence of inducer causes the HTH motifs to reverse their orientation.
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(1995)
Mol Biol
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Kamashev, D.1
Ebralidze, K.2
Esipova, N.G.3
Mirzabekov, A.D.4
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41
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0028076771
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Genetic studies of the lac repressor : Analysis of 4000 altered Escherichia coli lac repressors revealing essential and non-essential residues, as well as "spacers" which do not require a specific sequence
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Markiewicz P, Kleina LG, Cruz C, Ehret S, Miller JH. Genetic studies of the lac repressor : analysis of 4000 altered Escherichia coli lac repressors revealing essential and non-essential residues, as well as "spacers" which do not require a specific sequence. J Mol Biol. 240:1994;421-433.
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The roles of residues 5 and 9 of the recognition helix of lac repressor in lac operator binding
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Sartorius J, Lehming N, Kisters-Woike B, Von Wilken-Bergmann B, Müller-Hill B. The roles of residues 5 and 9 of the recognition helix of lac repressor in lac operator binding. J Mol Biol. 218:1991;313-321.
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43
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0025058598
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Lehming N, Sartorius J, Kisters-Woike B, Von Wilcken-Bergmann B, Müller-Hill B. Mutant lac repressors with new specificities hint at rules for protein-DNA recognition. EMBO J. 9:1990;615-621.
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of outstanding interest. The authors present the NMR structures of an extended fragment of the DNA-binding domain (residues 1-62) of the lac repressor with and without DNA. The hinge helix was found to form in the presence of DNA. The structure of the DNA-binding domain complexed to operator DNA shows a bend in the DNA which is similar to that seen in the crystallographic structure [5]. Attempts to account thermodynamically for the structural changes in the lac repressor upon DNA binding are made.
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