a 2010

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

MOTÁČKOVÁ, Veronika, Pavel KADEŘÁVEK, Lukáš ŽÍDEK, Hana ŠANDEROVÁ, Petr PADRTA et. al.

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

Odkazy

URL

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

RNA polymerase; delta subunit; gram-positive bacteria; structure; validation; structural homologues; dynamics

Příznaky

Mezinárodní význam
Změněno: 19. 10. 2010 10:54, Mgr. Veronika Papoušková, Ph.D.

Anotace

ORIG EN

V originále

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.

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
Zobrazeno: 12. 11. 2024 07:43