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Abstract
The conserved A:T base pair at the -11 position of the promoters in Escherichia coli is very sensitive to substitutions. In vitro transcription with the galP1 promoter having a natural or unnatural base in either strand at position -11 showed that only a purine base with no side group at C2 in the nontemplate strand is transcriptionally potent; neither a purine with an amino group at C2 nor a pyrimidine support transcription. The amino group at C6 in the omnipresent adenine at -11 does not play any role in promoting transcription. The nature of the base, complementary or noncomplementary, at -11 in the template strand also does not influence transcription. We propose that the adenine, by becoming extrahelical, interacts with an amino acid(s) of the 2.3-2.4 region of sigma for which an unsubstituted C2 hydrogen is critical.
Highlights
Accelerated PublicationTHE JOURNAL OF BIOLOGICAL CHEMISTRY Vol 279, No 17, Issue of April 23, pp. 16899 –16902, 2004
An Unsubstituted C2 Hydrogen of Adenine Is Critical and Sufficient at the ؊11 Position of a Promoter to Signal Base Pair Deformation*
If an amino acid side chain(s) in the 2.3–2.4 region makes a direct contact with the Ϫ11 adenine, either the interaction involves the C2 hydrogen or the substitution of the C2 hydrogen causes a steric problem for the interaction
Summary
THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol 279, No 17, Issue of April 23, pp. 16899 –16902, 2004. The open complex is competent to initiate polymerization of ribonucleotides according to the DNA sequences of the template strand (1– 4) Both DNA (Ϫ10 region of the promoter) and the multisubunit enzyme go through major conformational changes in becoming an open complex (4 –9). Several amino acid residues in the 2.3– 2.4 region of the subunit were inferred to make consequential contacts with bases in the Ϫ10 region of the promoter: Phe[427], Tyr[430], and Trp[433] in the formation of the open complex, Lys[414], Lys[415], Tyr[425], Phe[427], and Tyr[430] in binding to single-stranded DNA following DNA deformation, and Tyr[430] in the stabilization of the open complex (4, 16, 18 –27). We investigated the properties of the Ϫ11 base pair, which are critical in interacting with and in signaling base pair deformation
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