Structure of the bacterial RNA polymerase promoter specificity sigma subunit

Mol Cell. 2002 Mar;9(3):527-39. doi: 10.1016/s1097-2765(02)00470-7.


The sigma subunit is the key regulator of bacterial transcription. Proteolysis of Thermus aquaticus sigma(A), which occurred in situ during crystallization, reveals three domains, sigma(2), sigma(3), and sigma(4), connected by flexible linkers. Crystal structures of each domain were determined, as well as of sigma(4) complexed with -35 element DNA. Exposed surfaces of each domain are important for RNA polymerase binding. Universally conserved residues important for -10 element recognition and melting lie on one face of sigma(2), while residues important for extended -10 recognition lie on sigma(3). Genetic studies correctly predicted that a helix-turn-helix motif in sigma(4) recognizes the -35 element but not the details of the protein-DNA interactions. Positive control mutants in sigma(4) cluster in two regions, positioned to interact with activators bound just upstream or downstream of the -35 element.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Models, Molecular
  • Promoter Regions, Genetic*
  • Protein Structure, Tertiary*
  • Sigma Factor / chemistry*
  • Sigma Factor / genetics
  • Sigma Factor / metabolism
  • Thermus / enzymology*
  • Thermus / genetics
  • Transcription, Genetic


  • Bacterial Proteins
  • Sigma Factor
  • RNA polymerase sigma A
  • DNA-Directed RNA Polymerases

Associated data

  • PDB/1KU2
  • PDB/1KU3
  • PDB/1KU7