Highlights Structure of the bacterial RNA polymerase subunit/promoter 10 element DNA complex Base-specific interactions occur with two

o highly conserved bases flipped out of the DNA Results suggest that 10 element recognition and melting are coupled

Summary The key step in bacterial promoter opening is recognition of the 10 promoter element (T12A11T10A9A8T7 consensus sequence) by the RNA polymerase subunit. We determined crystal structures of domain 2 bound to single-stranded DNA bearing 10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every 10 element nucleotide. Base-specific interactions occur primarily with A11 and T7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the 10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by . These results provide a detailed structural basis for the critical roles of A11 and T7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Highlights Structure of the bacterial RNA polymerase subunit/promoter 10 element DNA complex Base-specific interactions occur with two highly conserved bases flipped out of the DNA Results suggest that 10 element recognition and melting are coupled

Summary The key step in bacterial promoter opening is recognition of the 10 promoter element (T12A11T10A9A8T7 consensus sequence) by the RNA polymerase subunit. We determined crystal structures of domain 2 bound to single-stranded DNA bearing 10 element sequences.

Extensive interactions occur between the protein and the DNA backbone of every 10 element nucleotide. Base-specific interactions occur primarily with A11 and T7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the 10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by . These results provide a detailed structural basis for the critical roles of A11 and T7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Highlights Structure of the bacterial RNA polymerase subunit/promoter 10 element DNA complex Base-specific interactions occur with two highly conserved bases flipped out of the DNA Results suggest that 10 element recognition and melting are coupled

Summary The key step in bacterial promoter opening is recognition of the 10 promoter element (T12A11T10A9A8T7 consensus sequence) by the RNA polymerase subunit. We determined crystal structures of domain 2 bound to single-stranded DNA bearing 10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every 10 element nucleotide. Base-specific interactions occur primarily with A11 and T7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the 10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by . These results provide a detailed structural basis for the critical roles of A11 and T7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Highlights Structure of the bacterial RNA polymerase subunit/promoter 10 element DNA complex Base-specific interactions occur with two highly conserved bases flipped out of the DNA Results suggest that 10 element recognition and melting are coupled

Summary The key step in bacterial promoter opening is recognition of the 10 promoter element (T12A11T10A9A8T7 consensus sequence) by the RNA polymerase subunit. We determined crystal structures of domain 2 bound to single-stranded DNA bearing 10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every 10 element nucleotide. Base-specific interactions occur primarily with A11 and T7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the 10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by . These results provide a detailed structural basis for the

critical roles of A11 and T7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Highlights Structure of the bacterial RNA polymerase subunit/promoter 10 element DNA complex Base-specific interactions occur with two highly conserved bases flipped out of the DNA Results suggest that 10 element recognition and melting are coupled

Summary The key step in bacterial promoter opening is recognition of the 10 promoter element (T12A11T10A9A8T7 consensus sequence) by the RNA polymerase subunit. We determined crystal structures of domain 2 bound to single-stranded DNA bearing 10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every 10 element nucleotide. Base-specific interactions occur primarily with A11 and T7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the 10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by . These results provide a detailed structural basis for the critical roles of A11 and T7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Highlights Structure of the bacterial RNA polymerase subunit/promoter 10 element DNA complex Base-specific interactions occur with two highly conserved bases flipped out of the DNA Results suggest that 10 element recognition and melting are coupled

Summary The key step in bacterial promoter opening is recognition of the 10 promoter element (T12A11T10A9A8T7 consensus sequence) by the RNA polymerase subunit. We determined crystal structures of domain 2 bound to single-stranded DNA bearing 10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every 10 element nucleotide. Base-specific interactions occur primarily with A11 and T7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the 10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by . These results provide a detailed structural basis for the critical roles of A11 and T7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Highlights Structure of the bacterial RNA polymerase subunit/promoter 10 element DNA complex

Base-specific interactions occur with two highly conserved bases flipped out of the DNA Results suggest that 10 element recognition and melting are coupled

Summary The key step in bacterial promoter opening is recognition of the 10 promoter element (T12A11T10A9A8T7 consensus sequence) by the RNA polymerase subunit. We determined crystal structures of domain 2 bound to single-stranded DNA bearing 10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every 10 element nucleotide. Base-specific interactions occur primarily with A11 and T7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the 10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by . These results provide a detailed structural basis for the critical roles of A11 and T7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.