Abstract
The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA bending and smaller DNA-induced changes in protein structure. N15 Cro makes fewer direct contacts and hydrogen bonds to bases, relying mostly on water-mediated and Van der Waals contacts to recognize the sequence. The recognition helices of N15 Cro and λ Cro make mostly nonhomologous and nonanalogous contacts. Interface alignment scores show that half-site binding geometries of N15 Cro and λ Cro are less similar to each other than to distantly related CI repressors. Despite this divergence, the Cro family shows several code-like protein-DNA sequence covariations. In some cases, orthologous genes can achieve a similar biological function using very different specific molecular interactions.
Original language | English (US) |
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Pages (from-to) | 7118-7129 |
Number of pages | 12 |
Journal | Nucleic acids research |
Volume | 47 |
Issue number | 13 |
DOIs | |
State | Published - Jul 26 2019 |
ASJC Scopus subject areas
- Genetics
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STRUCTURE OF N15 CRO COMPLEXED WITH CONSENSUS OPERATOR DNA
Hall, B. M. (Contributor), Roberts, S. A. (Contributor) & Cordes, M. H. J. (Contributor), Protein Data Bank (PDB), May 15 2019
DOI: 10.2210/pdb6ON0/pdb, https://www.wwpdb.org/pdb?id=pdb_00006on0
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