Structural Study of the Partially Disordered Full-Length δ Subunit of RNA Polymerase from Bacillus subtilis

Authors

  • Dr. Veronika Papoušková,

    1. Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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  • Dr. Pavel Kadeřávek,

    1. Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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  • Olga Otrusinová,

    1. Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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  • Alžbeta Rabatinová,

    1. Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague (Czech Republic)
    2. Faculty of Science, Charles University, Viničná 5, 128 44 Prague 2 (Czech Republic)
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  • Dr. Hana Šanderová,

    1. Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague (Czech Republic)
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  • Jiří Nováček,

    1. Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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  • Dr. Libor Krásný,

    1. Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague (Czech Republic)
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  • Prof. Vladimír Sklenář,

    1. Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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  • Dr. Lukáš Žídek

    Corresponding author
    1. Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
    • Faculty of Science, NCBR and CEITEC MU, Masaryk University, Kamenice 5, 625 00 Brno (Czech Republic)
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Abstract

The partially disordered δ subunit of RNA polymerase was studied by various NMR techniques. The structure of the well-folded N-terminal domain was determined based on inter-proton distances in NOESY spectra. The obtained structural model was compared to the previously determined structure of a truncated construct (lacking the C-terminal domain). Only marginal differences were identified, thus indicating that the first structural model was not significantly compromised by the absence of the C-terminal domain. Various 15N relaxation experiments were employed to describe the flexibility of both domains. The relaxation data revealed that the C-terminal domain is more flexible, but its flexibility is not uniform. By using paramagnetic labels, transient contacts of the C-terminal tail with the N-terminal domain and with itself were identified. A propensity of the C-terminal domain to form β-type structures was obtained by chemical shift analysis. Comparison with the paramagnetic relaxation enhancement indicated a well-balanced interplay of repulsive and attractive electrostatic interactions governing the conformational behavior of the C-terminal domain. The results showed that the δ subunit consists of a well-ordered N-terminal domain and a flexible C-terminal domain that exhibits a complex hierarchy of partial ordering.

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