title: X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase.
abstract: The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Demo
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.
authors.forename: Veronika
authors.initials: V
authors.lastname: Papoušková
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Komárek
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Kadeřávek
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.
authors.forename: Olga
authors.initials: O
authors.lastname: Otrusinová
authors.affiliation: Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Srb
authors.affiliation: Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic.
authors.forename: Alžbeta
authors.initials: A
authors.lastname: Rabatinová
authors.affiliation: Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic.
authors.forename: Libor
authors.initials: L
authors.lastname: Krásný
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic. Electronic address: lzidek@chemi.muni.cz.
authors.forename: Lukáš
authors.initials: L
authors.lastname: Žídek
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Sklenář
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5/A5, 62500 Brno, Czech Republic. Electronic address: michaw@chemi.muni.cz.
authors.forename: Michaela
authors.initials: M
authors.lastname: Wimmerová
mesh_terms: D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000201:enzymology; D018360:Crystallography, X-Ray / Q000379:methods*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D012321:DNA-Directed RNA Polymerases
keywords: N-terminal domain; Nuclear magnetic resonance; Protein crystallography; RNA polymerase; δ-Subunit