Publication details

Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria

Authors

MOTÁČKOVÁ Veronika KADEŘÁVEK Pavel ŽÍDEK Lukáš ŠANDEROVÁ Hana PADRTA Petr NOVÁČEK Jiří ŠVENKOVÁ Alžběta KORELUSOVÁ Jana ZAWADZKA-KAZIMIERCZUK Anna KAZIMIERCZUK Krzysztof KOŹMIŃSKI Wiktor KRÁSNÝ Libor SKLENÁŘ Vladimír

Year of publication 2010
Type Conference abstract
MU Faculty or unit

Faculty of Science

Citation
Description Architecture of RNA polymerase (RNAP) from B. subtilis and other gram-positive bacteria differs from its analogue from gram-negative bacteria in the presence of two additional subunits - omega1 and delta. The delta subunit is important for virulence of pathogens. It has been reported that the presence of delta subunit increases the transcription specificity and the efficiency of RNA synthesis. No structural information was available for the delta subunit due to the lack of sequence homology. As crystallization at structure genomics centers failed, we focused on the delta subunit in our NMR structural study. Because the C-terminal part of the delta subunit is unstructured and its peaks overlap as its sequence is highly repetitive, we first characterized the ordered N-terminal domain. Its structure was solved using a large set of high-quality NMR restraints, including 2341 NOE (544 long range), 384 RDC, and 33 13C CSA restraints from two aligning media (bacteriophage Pf1, 5% polyacrylamide gel). The calculations were run in CNS using a protocol modified in our lab to combine the SCULPTOR module with RECOORD scripts. Program CING was used to check the quality of the structures. The determined structure allowed us to identify unexpected structure homology of the N-terminal domain of delta subunit with several proteins from the Forkhead DNA/RNA-binding domain SCOP family and to propose residues interacting with the RNAP core. Relaxation dispersion revealed significant us motions in the interaction surface, supporting the induced-fit model of binding. The partially disordered full-size protein was then completely assigned using 5D non-uniformly sampled spectra and results of a preliminary analysis of its structure and dynamics will be presented.
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