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

MOTÁČKOVÁ, Veronika, Pavel KADEŘÁVEK, Lukáš ŽÍDEK, Hana ŠANDEROVÁ, Petr PADRTA, Jiří NOVÁČEK, Alžběta ŠVENKOVÁ, Jana KORELUSOVÁ, Anna ZAWADZKA-KAZIMIERCZUK, Krzysztof KAZIMIERCZUK, Wiktor KOŹMIŃSKI, Libor KRÁSNÝ and Vladimír SKLENÁŘ. Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria. In Joint EUROMAR 2010 and 17th ISMAR Conference. 2010.

Basic information

• Original name: Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria
• Name in Czech: Struktura a dynamika podjednotky RNA polymerazy specifické pro gram-pozitivní bakterie
• Name (in English): Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria
• Authors: MOTÁČKOVÁ, Veronika, Pavel KADEŘÁVEK, Lukáš ŽÍDEK, Hana ŠANDEROVÁ, Petr PADRTA, Jiří NOVÁČEK, Alžběta ŠVENKOVÁ, Jana KORELUSOVÁ, Anna ZAWADZKA-KAZIMIERCZUK, Krzysztof KAZIMIERCZUK, Wiktor KOŹMIŃSKI, Libor KRÁSNÝ and Vladimír SKLENÁŘ.
• Edition: Joint EUROMAR 2010 and 17th ISMAR Conference, 2010.

Other information

• Type of outcome: Conference abstract
• Field of Study: 10600 1.6 Biological sciences
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Organization unit: Faculty of Science
• Keywords in English: RNA polymerase; delta subunit; gram-positive bacteria; structure; validation; structural homologues; dynamics
• Tags: International impact

Abstract

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.

Abstract (in English)

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.

Links

• GA204/09/0583, research and development project: Name: Delta podjednotka RNA polymerázy z Gram pozitivních bakterií (Acronym: DELTA)

Investor: Czech Science Foundation

• GD301/09/H004, research and development project: Name: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny

Investor: Czech Science Foundation

• LC06030, research and development project: Name: Biomolekulární centrum

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment