Backbone dynamics of N-terminal Domain of the Delta Subunit of Bacterial RNA Polymerase

KADEŘÁVEK, Pavel, Carl DIEHL, Veronika MOTÁČKOVÁ, Lukáš ŽÍDEK, Libor KRÁSNÝ and Mikael AKKE. Backbone dynamics of N-terminal Domain of the Delta Subunit of Bacterial RNA Polymerase. In Structural Biology Network 13th Annual Conference. 2009.

Basic information

• Original name: Backbone dynamics of N-terminal Domain of the Delta Subunit of Bacterial RNA Polymerase
• Authors: KADEŘÁVEK, Pavel, Carl DIEHL, Veronika MOTÁČKOVÁ, Lukáš ŽÍDEK, Libor KRÁSNÝ and Mikael AKKE.
• Edition: Structural Biology Network 13th Annual Conference, 2009.

Other information

• Type of outcome: Conference abstract
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Organization unit: Faculty of Science

Abstract

The RNA polymerase consists of eight subunits. A dimer of two alpha subunits holds together two beta subunits which form the active site. The sigma subunit is responsible for both promoter recognition and ranscription initiation [1], whereas the roles of the two omega subunits are poorly understood. The delta subunit increases both the transcriptional specificity [2],[3],[4],[5],[6],[7] and the efficiency of RNA synthesis [5],[6],[7]. The delta subunit and one of the omega subunits are not conserved throughout all bacterial species. Here we present the backbone dynamics of the N-terminal domain of the delta subunit of bacterial RNA polymerase from Bacillus subtilis. The N-terminal domain of the delta subunit has a well-defined structure, while the C-terminal domain is unstructured and highly negatively charged. Here we focus on the isolated N-terminal domain, whose structure consists of an alpha helical core and a short beta sheet [8]. The standard set of 15-N relaxation experiments (R1,R2,NOE) were performed at two magnetic field (500MHz, 600MHz) in order to analyze fast ns-ps backbone motions. The relaxation experiments were acquired at two temperatures (300K, 280K) in order to get a more comprehensive description. Slow motions on the ms-us timescale were investigated by CPMG and T1rho relaxation dispersion experiments. An interesting dynamic behavior was revealed in the region involving the short beta sheet and its proximity. REFERENCES: [1] Cramer P., Current Opinion in Structural Biology, 12, 89-97, 2002 [2] Achberger E.C., Whiteley H.R., Journal of Biological Chemistry, 256, 7424-7432, 1981 [3] Achberger E.C., Tahara M., Whiteley H.R., Journal of Bacteriology, 150, 977-980, 1982 [4] Dobinson K.F., Spiegelman G.B., Biochemistry, 26, 8206-8213, 1987 [5] Juang Y.L., Helmann J.D., Journal of Molecular Biology, 239, 1-14, 1994 [6] Juang Y.L., Helmann J.D., Biochemistry, 34, 14270-14270, 1995 [7] Juang Y.L., Helmann J.D., Biochemistry, 34, 8465-8473, 1995 [8] Motáčková V., Šanderová H., Nováček J., Žídek L.,Sklenář V., Krasný L., (poster), 7th Discussions in Structural Molecular Biology, Nové Hrady, 2009