The σ54 RNA polymerase holoenzyme functions in enhancer-dependent transcription. The structural organization of the σ54 subunit of bacterial RNA polymerase in solution is analyzed by synchrotron x-ray scattering. Scattering patterns are collected from the full-length protein and from a large fragment able to bind the core RNA polymerase, and their low resolution shapes are restored using two ab initio shape determination techniques. The σ54 subunit is a highly elongated particle, and the core binding fragment can be unambiguously positioned inside the full-length protein. The boomerang-like shape of the core binding fragment is similar to that of the atomic model of a fragment of the Escherichia coli σ70 protein, indicating that, although the σ54 and σ70 factors are unrelated by primary sequence, they may share some structural similarity. Potential DNA binding surfaces of σ54 are also predicted by comparison with the σ54 core binding fragment.
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Svergun, D. I., Malfois, M., Koch, M. H. J., Wigneshweraraj, S. R., & Buck, M. (2000). Low resolution structure of the σ54 transcription factor revealed by x- ray solution scattering. Journal of Biological Chemistry, 275(6), 4210–4214. https://doi.org/10.1074/jbc.275.6.4210