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 a Vladimír SKLENÁŘ. Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria. In Joint EUROMAR 2010 and 17th ISMAR Conference. 2010.

Základní údaje

• Originální název: Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria
• Název česky: Struktura a dynamika podjednotky RNA polymerazy specifické pro gram-pozitivní bakterie
• Název anglicky: Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria
• Autoři: 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 a Vladimír SKLENÁŘ.
• Vydání: Joint EUROMAR 2010 and 17th ISMAR Conference, 2010.

Další údaje

• Typ výsledku: Konferenční abstrakt
• Obor: 10600 1.6 Biological sciences
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Organizační jednotka: Přírodovědecká fakulta
• Klíčová slova anglicky: RNA polymerase; delta subunit; gram-positive bacteria; structure; validation; structural homologues; dynamics
• Příznaky: Mezinárodní význam

Anotace

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.

Anotace anglicky

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.

Návaznosti

• GA204/09/0583, projekt VaV: Název: Delta podjednotka RNA polymerázy z Gram pozitivních bakterií (Akronym: DELTA)

Investor: Grantová agentura ČR, Delta podjednotka RNA polymerázy z Gram pozitivních bakterií

• GD301/09/H004, projekt VaV: Název: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny

Investor: Grantová agentura ČR, Molekulární a strukturní biologie vybraných cytostatik. Od mechanických studií k chemoterapii rakoviny

• LC06030, projekt VaV: Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

• MSM0021622413, záměr: Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím