Activator catabolite protein

Notice also the big bend in the DNA at the thymine-adenine base pair at center. References A. Kolb, S. Busby, H. Buc, S. Garges and S. Adhya : Transcriptional regulation by cAMP and its receptor protein. Annual Review of Biochemistry 62 , pp. Busby and R. Ebright : Transcription activation by catabolite activator protein. Journal of Molecular Biology , pp.

About Molecule of the Month. CAP exhibits strong sequence preferences at seven positions within each DNA half-site: positions 1, 2, and 4—8 boxed positions in Fig 1b [ 11 , 15 , 16 , 17 ].

Sequence preferences at three positions within each DNA half-site--positions 5, 7, and are accounted for by direct amino acid-base contacts Fig 1b [ 12 , 13 , 14 , 18 , 19 , 20 ].

In contrast, sequence preferences at the remaining positions occur in the absence of amino acid-base contacts and thus must involve indirect readout Fig 1b [ 12 , 13 ]. The primary kink is located between positions 6 and 7 Fig 1b. The structures were obtained from isomorphous crystals with space-group symmetry P 3 1 The results indicate that a given overall DNA bend angle can be achieved through very different local DNA-helical parameters at the primary-kink site.

We note, however, a complexity in the kinking vs. The DNA fragments in the two structures differ in multiple respects, including lengths 38 vs. Therefore, in this case, it is not possible to deduce the basis for the difference in local DNA-helical parameters at the primary kink site. An estimate of 15o was obtained in cyclization assays employing tandem arrays of DNA sites [ 26 ].

Simple CAP-dependent promoters-- i. Activation by recruitment does not requires conformational signalling within or through the target, does not require extensive, high-information-content interactions between activator and target, and entails modest net interaction energies between activator and target--interaction energies comparable to the magnitude of activation [ 45 , 46 ]. The model is consistent with all available experimental information and provides a structural framework for understanding Class I CAP-dependent transcription.

In each panel, a molecular surface representation is shown at left; and a stereodiagram with a ribbon representation is shown at right. The DNA template and nontemplate strands are in red and pink. The resulting model is consistent with all available experimental information and provides an indispensable structural framework for understanding Class II CAP-dependent transcription.

DNA binding and transcription activation by CAP should be amenable to a complete structural description. Based on recent experience, progress is likely to be rapid. We thank A.

Kapanidis, A. Napoli and N. Naryshkin for discussion. L , GM W. Olson and D. Levy and R. National Center for Biotechnology Information , U. Curr Opin Struct Biol. Author manuscript; available in PMC Oct Catherine L.

Lawson , 1 David Swigon , 1 Katsuhiko S. Murakami , 2 Seth A. Darst , 3 Helen M. Berman , 1, 4 and Richard H. Ebright 1, 4, 5. Katsuhiko S. Seth A. Helen M. Richard H. Author information Copyright and License information Disclaimer. Copyright notice. The publisher's final edited version of this article is available at Curr Opin Struct Biol. See other articles in PMC that cite the published article. Warning You are using a web browser that we do not support.

Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox. Asymmetric Unit. Macromolecule Content Total Structure Weight: This is version 1.