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Functional roles of the pre‐sensor I insertion sequence in an AAA+ bacterial enhancer binding protein
Author(s) -
Burrows Patricia C.,
Schumacher Jörg,
Amartey Samuel,
Ghosh Tamaswati,
Burgis Timothy A.,
Zhang Xiaodong,
Nixon B. Tracy,
Buck Martin
Publication year - 2009
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/j.1365-2958.2009.06744.x
Subject(s) - biology , atp hydrolysis , nucleotide , sequence alignment , enhancer , biochemistry , peptide sequence , biophysics , microbiology and biotechnology , genetics , computational biology , atpase , transcription factor , gene , enzyme
Summary Molecular machines belonging to the AAA+ superfamily of ATPases use NTP hydrolysis to remodel their versatile substrates. The presence of an insertion sequence defines the major phylogenetic pre‐sensor I insertion (pre‐SIi) AAA+ superclade. In the bacterial σ 54 ‐dependent enhancer binding protein phage shock protein F (PspF) the pre‐SIi loop adopts different conformations depending on the nucleotide‐bound state. Single amino acid substitutions within the dynamic pre‐SIi loop of PspF drastically change the ATP hydrolysis parameters, indicating a structural link to the distant hydrolysis site. We used a site‐specific protein–DNA proximity assay to measure the contribution of the pre‐SIi loop in σ 54 ‐dependent transcription and demonstrate that the pre‐SIi loop is a major structural feature mediating nucleotide state‐dependent differential engagement with Eσ 54 . We suggest that much, if not all, of the action of the pre‐SIi loop is mediated through the L1 loop and relies on a conserved molecular switch, identified in a crystal structure of one pre‐SIi variant and in accordance with the high covariance between some pre‐SIi residues and distinct residues outside the pre‐SIi sequence.