title: DNA recognition by a σ(54) transcriptional activator from Aquifex aeolicus.
abstract: Transcription initiation by bacterial σ(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of σ(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for σ(54) regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.
authors.affiliation: Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.
authors.forename: Natasha K
authors.initials: NK
authors.lastname: Vidangos
authors.affiliation: Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.
authors.forename: Johanna
authors.initials: J
authors.lastname: Heideker
authors.affiliation: Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.
authors.forename: Artem
authors.initials: A
authors.lastname: Lyubimov
authors.affiliation: Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.
authors.forename: Meindert
authors.initials: M
authors.lastname: Lamers
authors.affiliation: Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Box 951569, Los Angeles, CA 90095, USA.
authors.forename: Yixin
authors.initials: Y
authors.lastname: Huo
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Pelton
authors.affiliation: Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.
authors.forename: Jimmy
authors.initials: J
authors.lastname: Ton
authors.affiliation: Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Box 951569, Los Angeles, CA 90095, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Gralla
authors.affiliation: Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA.
authors.forename: James
authors.initials: J
authors.lastname: Berger
authors.affiliation: Department of Chemistry, University of California, MC-1460, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: dewemmer@berkeley.edu.
authors.forename: David E
authors.initials: DE
authors.lastname: Wemmer
mesh_terms: D001419:Bacteria / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D003850:Deoxyribonuclease I / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry*; D035021:Factor For Inversion Stimulation Protein / Q000737:chemistry*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D051922:PII Nitrogen Regulatory Proteins / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D051877:RNA Polymerase Sigma 54 / Q000737:chemistry*; D014157:Transcription Factors / Q000737:chemistry*; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; D051922:PII Nitrogen Regulatory Proteins; D011506:Proteins; D014157:Transcription Factors; C497876:glnG protein, E coli; D004247:DNA; D051877:RNA Polymerase Sigma 54; D003850:Deoxyribonuclease I
keywords: DNA complex; DNA-binding domain; Fis; NtrC; sequence-specific recognition