The bacteriophage D108 Ner repressor binds a conformationally distinct operator.

G Kukolj; M S DuBow

doi:10.1007/s004380051206

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PubMed · 10852480

The bacteriophage D108 Ner repressor binds a conformationally distinct operator.

G Kukolj·M S DuBow

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Abstract

The Ner protein encoded by the transposable coliphage D108, an 8.6 kDa lambda Cro-like repressor, binds to an operator spanning 50 bp of DNA. The distinguishing features of this operator are two perfect 11-bp inverted repeats (5'-CCGTGAGCTAC-3') that are separated by an 8-bp AT-rich spacer. Hyperreactivity of the ner operator to potassium permanganate and the hydroxyl radical indicate that the AT-rich spacer assumes a variant conformation consistent with a bend. Using an electrophoretic mobility shift assay, we demonstrated that Ner does not display significant affinity for a single 11-bp site. Furthermore, DNase I protection analysis and circular-permutation binding assays reveal that alterations in the length and sequence of the AT-rich spacer that separates the 11-bp inverted repeats significantly alter Ner-operator interactions, and demonstrate that the intrinsically bent ner operator is conformationally altered upon protein binding.

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Bacteriophages Base Sequence Binding Sites DNA, Ribosomal DNA-Binding Proteins Molecular Sequence Data Operon Repetitive Sequences, Nucleic Acid Repressor Proteins Restriction Mapping Transposases Viral Proteins Viral Regulatory and Accessory Proteins Journal Article Research Support, Non-U.S. Gov't

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G Kukolj, M S DuBow. 2000. The bacteriophage D108 Ner repressor binds a conformationally distinct operator.. https://doi.org/10.1007/s004380051206

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