title: Structural basis of transcription initiation.
abstract: During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 Å resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, σ(A), and a promoter DNA fragment corresponding to the transcription bubble and downstream double-stranded DNA of the RNAP-promoter open complex. The structures show that σ recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases and that RNAP recognizes the -4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between σ and template-strand single-stranded DNA (ssDNA) preorganize template-strand ssDNA to engage the RNAP active center.
authors.affiliation: Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Yu
authors.initials: Y
authors.lastname: Feng
authors.forename: Sujoy
authors.initials: S
authors.lastname: Chatterjee
authors.forename: Steve
authors.initials: S
authors.lastname: Tuske
authors.forename: Mary X
authors.initials: MX
authors.lastname: Ho
authors.forename: Eddy
authors.initials: E
authors.lastname: Arnold
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
mesh_terms: D018360:Crystallography, X-Ray; D004277:DNA, Single-Stranded / Q000737:chemistry; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D015964:Gene Expression Regulation, Bacterial; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012808:Sigma Factor / Q000737:chemistry*; D016963:Thermus thermophilus / Q000201:enzymology* / Q000235:genetics*; D061785:Transcription Initiation, Genetic
chemical_list: D004277:DNA, Single-Stranded; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases