title: The C-terminal RpoN domain of sigma54 forms an unpredicted helix-turn-helix motif similar to domains of sigma70.
abstract: The "sigma" subunit of prokaryotic RNA polymerase allows gene-specific transcription initiation. Two sigma families have been identified, sigma70 and sigma54, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the sigma70-type factors have been well characterized structurally by x-ray crystallography, no high resolution structural information is available for the sigma54-type factors. Here we present the NMR-derived structure of the C-terminal domain of sigma54 from Aquifex aeolicus. This domain (Thr-323 to Gly-389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the sigma70-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. The homology of this structure with other DNA-binding proteins, combined with previous biochemical data, suggests how the C-terminal domain of sigma54 binds to DNA.
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Michaeleen
authors.initials: M
authors.lastname: Doucleff
authors.forename: Lawrence T
authors.initials: LT
authors.lastname: Malak
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Pelton
authors.forename: David E
authors.initials: DE
authors.lastname: Wemmer
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry*; D019077:Helix-Turn-Helix Motifs; D007709:Klebsiella / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010957:Plasmids / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D051877:RNA Polymerase Sigma 54 / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012808:Sigma Factor / Q000737:chemistry*; D013237:Stereoisomerism
chemical_list: D029968:Escherichia coli Proteins; D012808:Sigma Factor; C497751:rpoN protein, E coli; D004247:DNA; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54