title: Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain.
abstract: The dynamic properties of the C-terminal one-third of the alpha subunit of RNA polymerase were investigated. The intact alpha subunit exhibited almost the same NMR spectral pattern as the isolated C-terminal fragment, indicating that the C-terminal domain retains the same conformation as the isolated fragment, and that its motion is independent of that of the associated N-terminal domain. Analysis of the NMR dynamics data for the intact alpha subunit indicated that at least 13 residues between the N and C-terminal domains show distinctly higher motional flexibility than the structured parts. This flexible linker may endow the C-terminal domain with locational freedom in different kinds of initiation complex. The dynamics data also revealed that the residues in the contact site for DNA and transcription factors exhibited higher mobility than other secondary structural elements.
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Japan.
authors.forename: Y H
authors.initials: YH
authors.lastname: Jeon
authors.forename: T
authors.initials: T
authors.lastname: Yamazaki
authors.forename: T
authors.initials: T
authors.lastname: Otomo
authors.forename: A
authors.initials: A
authors.lastname: Ishihama
authors.forename: Y
authors.initials: Y
authors.lastname: Kyogoku
mesh_terms: D000595:Amino Acid Sequence; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D010446:Peptide Fragments; D012321:DNA-Directed RNA Polymerases