Escherichia coli lac repressor is elongated with its operator DNA binding domains located at both ends

McKay, David; Pickover, Clifford A.; Steitz, Thomas A.

doi:10.1016/0022-2836(82)90465-x

Cited by 38 publications

(34 citation statements)

References 17 publications

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“…The difference between this result and that in [14] may be explained taking into account the fact that in our experiments the concentration of lac operator fragment is several orders of magnitude larger than those used in the nitrocellulose filter experiments. The finding of a complex containing 2 operators is in perfect agreement with the model of lac repressor proposed in [17,18].…”

Section: Resultssupporting

confidence: 87%

Binding of lac repressor induces different conformational changes on operator and non‐operator DNAs

Culard

Maurizot

1982

FEBS Letters

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Section: Resultssupporting

confidence: 87%

Binding of lac repressor induces different conformational changes on operator and non‐operator DNAs

Culard

Maurizot

1982

FEBS Letters

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“…These dimensions are closely similar to those obtained by electron microscopy [55,561, and the volume enclosed by these dimensions (2.19X10-19 cm') is comparable to the 'molar mass volume' computed from the amino acid sequence, assuming a partial specific volume of 0.73 cm' g-' (1.89X10-" cm') [51]. If [51], the DNA-distal subunits of the tetramer are likely to be 2 4.0 nm from the DNA surface. This would place these subunits outside of the volume in which ionic concentrations are strongly perturbed.…”

supporting

confidence: 68%

“…Since the wild-type tetramer has roughly twice the molar mass of the lad-18 dimer, the small difference in the aggregate ion stoichiometries of the DNA-binding reactions of these proteins is striking. nm [51]. If, as proposed by…”

Section: Comparison Of Tetrameric and Dimeric Forms Of Lac Repressormentioning

confidence: 99%

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Analysis of the Thermodynamic Linkage of DNA Binding and Ion Binding for Dimeric and Tetrameric forms of the Lac Repressor

Stickle

Liu

Fried

1994

European Journal of Biochemistry

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The salt concentration dependences of the observed association constants (Kobe) for the binding of wild-type lac repressor tetramer and the dimeric lad-18 mutant repressor to lactose operator DNA were compared. For both proteins, the data are consistent with a class of linkage models in which ion binding by the protein is driven by differences in the ionic concentrations in bulk solution and in the volume near the DNA surface. The models that best agree with the data are those in which ion-binding reactions are cooperative. In spite of close agreement between these models and the data, the determination of ion stoichiometries and apparent ion-binding affinities requires additional mechanistic or structural information. The simplest ion-binding mechanism consistent with the data is compatible with a current structural model of the repressor-operator complex. At salt concentrations in excess of 50 mM, at which cation displacement from the DNA and anion displacement from the protein are expected to dominate, similar ion stoichiometries are found for the DNA binding of dimeric and tetrameric repressors. This supports the notion that the DNA contacts of these proteins are homologous. At lower salt concentrations, in which cation binding by the proteins is expected to be significant, the net ion stoichiometry of wild-type repressor binding is slightly greater than that of the lad-18 mutant. This difference may reflect the availability of ion-binding sites in the distal subunits of tetramer that are not present in the dimer, or may be a consequence of the involvement of ion binding in the dimer/monomer equilibrium.The observed equilibrium association constant (Kobs) for protein-nucleic-acid interactions is strongly dependent on the concentration and identity of ions present in the surrounding solution. The thermodynamics of the influence of ions on protein -nucleic-acid interactions has been described by If ion-binding reactions of protein and DNA are the only significant contributors to the influence of the concentration of a single monovalent salt (MX) on Koba, then the following relationship is predicted P I :where Am = the number of cations gained by the protein upon binding, An = the number of anions gained by the protein upon binding, and Aq = the number of cations gained by nucleic acid upon binding. [MX]. One explanation that is consistent with this observation is that it is due to the displacement, by protein binding, of cations from the negatively-charged nucleic acid surface ( A q < 0), and that ion-binding by the protein does not contribute (Am = An = 0). Since the cation concentration near the nucleic acid surface is almost independent of the bulk salt concentration for 10 mM d [MX]

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“…Probably one pair of twofold-related subunits of the repressor tetramer makes contact with one operator (43)(44)(45)(46)(47)(48) and, in addition, the second pair of twofold-related subunits constitutes a second operator-binding site, explaining the observed stoichiometry oftwo operators bound per repressor tetramer (49,50). We postulate that a pair of twofoldrelated a-helices lies within successive major grooves of the DNA, as is the case for the cro protein (4).…”

mentioning

confidence: 99%

Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor.

Matthews¹,

Ohlendorf²,

Anderson³

et al. 1982

Proc. Natl. Acad. Sci. U.S.A.

132

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It is shown that the amino acid sequence and the DNA gene sequence of the 25 amino-terminal residues of the lac repressor protein of Escherichia coli are homologous with the sequences of five DNA-binding proteins: the cro repressor proteins from phage A and phage 434, the cI and cdi proteins from phage A, and the repressor protein from Salmonella phage P22. The region of homology between lac repressor and the other proteins coincides with the principal DNA-binding region ofcro repressor. In particular, residues Tyr-17 through Gln-26 oflac repressor correspond to the a-helix Gln-27 through Ala-36 of cro repressor, which we have postulated to bind within the major groove of the DNA Fig. 1 shows a comparison of the amino-terminal sequences of a series of proteins that bind to sequence-specific regions of double-stranded DNA (5). cro and 434-cro are small repressor proteins from bacteriophage A and bacteriophage 434, respectively (10-13). "cI" (often referred to as A repressor) and "P22" are larger repressor proteins from phage A and from Salmonella phage P22, respectively, that, under different circumstances, can mediate positive or negative control of gene transcription (14-18). "clI" is also larger than cro and, in conjunction with another protein (cIII), acts as a positive regulator of transcription in bacteriophage A (16,17,19,20). With the exception of cro and cI, these five proteins all recognize different sequences on the DNA.As can be seen in Fig. 1, there is extensive amino acid sequence homology between the five DNA-binding proteins. The correspondence between the five proteins can also be seen in the DNA gene sequences that code for the respective polypeptides, and, on the basis of this sequence homology, we have argued (5) that these proteins all have in common a region of tertiary structure corresponding to the segments labeled al, a2, and a3. In the cro structure, al and a2 are "structural" a-helices, whereas a3 is the "DNA recognition" a-helix, which we have postulated to lie within the major groove of B-form DNA and to be primarily responsible for the specific recognition of the DNA by the protein (4).A series ofcomparisons ofboth the amino acid sequence . (21,22) and the DNA coding sequence (23) indicates that the lac repressor protein from E. coli ("lac") may also have structural features in common with the other DNA-binding proteins. In Fig. 1 we have included the first 38 amino acids of lac, aligned to maximize the homology with the other proteins. The homology is most striking in the region 19-32 of cro (9-22 of lac), where Gly-24 is invariant and Ala-20 and Val-25. of cro, which are conserved in four of the five proteins, also occur in lac.The homology between lac and the other proteins can also be seen at the level of the DNA sequences that code for the respective polypeptides. The publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this f...

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Escherichia coli lac repressor is elongated with its operator DNA binding domains located at both ends

Cited by 38 publications

References 17 publications

Binding of lac repressor induces different conformational changes on operator and non‐operator DNAs

Binding of lac repressor induces different conformational changes on operator and non‐operator DNAs

Analysis of the Thermodynamic Linkage of DNA Binding and Ion Binding for Dimeric and Tetrameric forms of the Lac Repressor

Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor.

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