RNA DNA discrimination by the antitermination protein NusB.
The regulation of ribosomal RNA biosynthesis in Escherichia coli by antitermination requires binding of NusB protein to a dodecamer sequence designated boxA on the nascent RNA. The affinity of NusB protein for boxA RNA exceeds that for the homologous DNA segment by more than three orders of magnitude as shown by surface plasmon resonance measurements. DNA RNA discrimination by NusB protein was shown to involve methyl groups (i.e. discrimination of uracil versus thymine) and 2' hydroxyl groups (i.e. discrimination of ribose versus deoxyribose side-chains) in the RNA motif. Ligand perturbation experiments monitored by 1H15N correlation NMR experiments identified amide NH groups whose chemical shifts are affected selectively by ribose/deoxyribose exchange in the 5' and the central part of the dodecameric boxA motif respectively. The impact of structural modification of the boxA motif on the affinity for NusB protein as observed by 1H15N heterocorrelation was analysed by a generic algorithm.
Mühlberger
René
R
Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstr. 4, D-85747, Garching, Germany.
Robelek
Rudolf
R
Eisenreich
Wolfgang
W
Ettenhuber
Christian
C
Sinner
Eva Kathrin
EK
Kessler
Horst
H
Bacher
Adelbert
A
Richter
Gerald
G
D001426:Bacterial Proteins / Q000502:physiology*; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000502:physiology*; D012689:Sequence Homology, Nucleic Acid; D020349:Surface Plasmon Resonance; D014157:Transcription Factors / Q000502:physiology*
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C074952:NusB protein, E coli; D016601:RNA-Binding Proteins; D014157:Transcription Factors; C064872:antiterminator proteins, Bacteria; D012313:RNA; D004247:DNA