3UGP

Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TATAAT)

Summary for 3UGP

• Entry DOI: 10.2210/pdb3ugp/pdb
• Related: 3UGO
• Descriptor: RNA polymerase sigma factor, 5'-D(*TP*GP*TP*AP*TP*AP*AP*TP*GP*GP*G)-3', POTASSIUM ION, ... (4 entities in total)
• Functional Keywords: protein-dna complex, bacterial promoter opening, g-quartet, g-quadruplex, dna binding, transcription-dna complex, transcription/dna
• Biological source: Thermus aquaticus
• Total number of polymer chains: 3
• Total formula weight: 35090.40

Authors

Feklistov, A.,Darst, S.A. (deposition date: 2011-11-02, release date: 2011-12-07, Last modification date: 2023-09-13)

Primary citation

Feklistov, A.,Darst, S.A.
Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit.
Cell(Cambridge,Mass.), 147:1257-1269, 2011

PubMed 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.

PubMed: 22136875
DOI: 10.1016/j.cell.2011.10.041

Experimental method

X-RAY DIFFRACTION (2.697 Å)