Summary information and primary citation

PDB-id
3ugo; SNAP-derived features in text and JSON formats; DNAproDB
Class
transcription-DNA
Method
X-ray (2.096 Å)
Summary
Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (tacaat)
Reference
Feklistov A, Darst SA (2011): "Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit." Cell(Cambridge,Mass.), 147, 1257-1269. doi: 10.1016/j.cell.2011.10.041.
Abstract
The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ 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 A(-11) and T(-7), 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 σ. These results provide a detailed structural basis for the critical roles of A(-11) and T(-7) in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Cartoon-block schematics in six views (download the tarball)

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