title: Crystal structure ofAquifex aeolicusσNbound to promoter DNA and the structure of σN-holoenzyme.
abstract: The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σNfragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σNThe structure allowed us to build and refine an improved σN-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σN-holoenzyme model reveals a conserved interdomain interface within σNthat, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σNin blocking transcription activity and in maintaining the activator sensitivity of σN.
authors.affiliation: Laboratory for Molecular Biophysics, The Rockefeller University, New York, NY 10065.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Campbell
authors.affiliation: Laboratory for Molecular Biophysics, The Rockefeller University, New York, NY 10065.
authors.forename: Shreya
authors.initials: S
authors.lastname: Kamath
authors.affiliation: Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439.
authors.forename: Kanagalaghatta R
authors.initials: KR
authors.lastname: Rajashankar
authors.affiliation: Laboratory for Molecular Biophysics, The Rockefeller University, New York, NY 10065.
authors.forename: Mengyu
authors.initials: M
authors.lastname: Wu
authors.affiliation: Laboratory for Molecular Biophysics, The Rockefeller University, New York, NY 10065; darst@rockefeller.edu.
authors.forename: Seth A
authors.identifier: 0000-0002-8241-3153
authors.initials: SA
authors.lastname: Darst
mesh_terms: D001419:Bacteria / Q000737:chemistry / Q000201:enzymology; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics; D020035:Holoenzymes / Q000737:chemistry* / Q000235:genetics; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics; D014158:Transcription, Genetic; D015533:Transcriptional Activation / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D020035:Holoenzymes; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases
keywords: RNA polymerase; X-ray crystallography; transcription; σ54; σN