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Molecular modeling of the cI repressor of bacteriophage ɛ 34
Author(s) -
Goodson Richardria,
McGee Lauren,
Gildea Logan,
Brooks Ryan,
Villafane Robert,
Jackson Doba
Publication year - 2019
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2019.33.1_supplement.779.13
Subject(s) - repressor , dna , gene , biology , genetics , dna binding domain , bacteriophage , homology (biology) , homologous chromosome , dna binding protein , microbiology and biotechnology , transcription factor , escherichia coli
Gene 46 of ɛ 34 encodes a protein that is similar to other phage repressors. It has a C‐terminal protease domain which is about 80% identical to the repressors of phage λ (which infects E. coli), but its DNA binding N‐terminal portion is only about 50% identical to its closest known relatives in phages λ, P22, and Lex A. The N‐terminal DNA‐binding domain is homologous to the HTH_XRE family of DNA‐binding domains [1]. We specifically looked at the N‐terminal domain of the cI with its homology to the HTH_XRE DNA binding proteins (also called the Cro/cI type HTH domain). To this date, 19 unique structures have been determined and are deposited into the Protein Data Bank (PDB). The HTH_XRE family of proteins has not been reviewed in the past 10 years despite the historical significance of its members as being the earliest members of the conserved class of DNA binding domains. We used the SWISS‐MODEL server to generate a series of homology models with and without DNA of to investigate how this protein interacts with its cognate DNA sequence. Presented in another, study, our bioinformatic and experimental studies have determined the 17 bp asymmetric site that interacts with the cI repressor. Our preliminary models have revealed some unique protein‐DNA contacts of the cI repressor that are not found in other homologous proteins (cI of λ, Φ11, 434, SinR, CopR, and Cro). The goal is to eventually initiate a structure‐function study and determine the three‐dimensional structure of this repressor. This project was done as a collaborative venture between two laboratories, Huntingdon College (Dr. Doba Jackson) and Alabama State University (laboratory of Dr. Robert Villafane). This project is in line with Dr. Robert Villafane's research into the Genomic analysis of bacteriophage ɛ 34 of Salmonella enteric serovar Anatum. Support or Funding Information Support for this project was provided by Alabama State University and Huntingdon College. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .