X-ray vs. NMR structure of N-terminal domain of delta-subunit
of RNA polymerase

J 2014

X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase

DEMO, Gabriel, Veronika PAPOUŠKOVÁ, Jan KOMÁREK, Pavel KADEŘÁVEK, Olga OTRUSINOVÁ et. al.

Základní údaje

Originální název

X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase

Autoři

DEMO, Gabriel (703 Slovensko, domácí), Veronika PAPOUŠKOVÁ (203 Česká republika, domácí), Jan KOMÁREK (203 Česká republika, domácí), Pavel KADEŘÁVEK (203 Česká republika, domácí), Olga OTRUSINOVÁ (203 Česká republika, domácí), Pavel SRB (203 Česká republika, domácí), Alzbeta RABATINOVA (703 Slovensko), Libor KRÁSNÝ (203 Česká republika), Lukáš ŽÍDEK (203 Česká republika, domácí), Vladimír SKLENÁŘ (203 Česká republika, domácí) a Michaela WIMMEROVÁ (203 Česká republika, garant, domácí)

Vydání

Journal of Structural Biology, San Diego, Academic Press, 2014, 1047-8477

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.231

Kód RIV

RIV/00216224:14740/14:00073722

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1016/j.jsb.2014.06.001

UT WoS

000340217300008

Klíčová slova anglicky

N-terminal domain; Nuclear magnetic resonance; Protein crystallography; RNA polymerase; delta-Subunit

Štítky

kontrola MP, rivok, SCOPUS

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 22. 10. 2014 15:09, Martina Prášilová

Anotace

V originále

The crystal structure of the N-terminal domain of the RNA polymerase delta subunit (Ndelta) from Bacillus subtilis solved at a resolution of 2.0 A 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 beta 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 Ndelta, 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 Ni2+ 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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.30.0009, projekt VaV

Název: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GA13-16842S, projekt VaV

Název: PODJEDNOTKY URČUJÍCÍ DNA SPECIFICITU BAKTERIÁLNÍ RNA POLYMERÁZY S FLEXIBILNÍMI DOMÉNAMI: FUNKCE A DYNAMIKA

Investor: Grantová agentura ČR, Podjednotky urcující DNA specificitu bakteriální RNA polymerázy s flexibilními doménami: funkce a dynamika

Citovat

DEMO, Gabriel, Veronika PAPOUŠKOVÁ, Jan KOMÁREK, Pavel KADEŘÁVEK, Olga OTRUSINOVÁ, Pavel SRB, Alzbeta RABATINOVA, Libor KRÁSNÝ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Michaela WIMMEROVÁ. X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase. Journal of Structural Biology. San Diego: Academic Press, 2014, roč. 187, č. 2, s. 174-186. ISSN 1047-8477. Dostupné z: https://dx.doi.org/10.1016/j.jsb.2014.06.001.

@article{1188082,
   author = {Demo, Gabriel and Papoušková, Veronika and Komárek, Jan and Kadeřávek, Pavel and Otrusinová, Olga and Srb, Pavel and Rabatinova, Alzbeta and Krásný, Libor and Žídek, Lukáš and Sklenář, Vladimír and Wimmerová, Michaela},
   article_location = {San Diego},
   article_number = {2},
   doi = {http://dx.doi.org/10.1016/j.jsb.2014.06.001},
   keywords = {N-terminal domain; Nuclear magnetic resonance; Protein crystallography; RNA polymerase; delta-Subunit},
   language = {eng},
   issn = {1047-8477},
   journal = {Journal of Structural Biology},
   title = {X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase},
   url = {http://www.sciencedirect.com/science/article/pii/S1047847714001373},
   volume = {187},
   year = {2014}
}

TY  - JOUR
ID  - 1188082
AU  - Demo, Gabriel - Papoušková, Veronika - Komárek, Jan - Kadeřávek, Pavel - Otrusinová, Olga - Srb, Pavel - Rabatinova, Alzbeta - Krásný, Libor - Žídek, Lukáš - Sklenář, Vladimír - Wimmerová, Michaela
PY  - 2014
TI  - X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase
JF  - Journal of Structural Biology
VL  - 187
IS  - 2
SP  - 174-186
EP  - 174-186
PB  - Academic Press
SN  - 10478477
KW  - N-terminal domain
KW  - Nuclear magnetic resonance
KW  - Protein crystallography
KW  - RNA polymerase
KW  - delta-Subunit
UR  - http://www.sciencedirect.com/science/article/pii/S1047847714001373
L2  - http://www.sciencedirect.com/science/article/pii/S1047847714001373
N2  - The crystal structure of the N-terminal domain of the RNA polymerase delta subunit (Ndelta) from Bacillus subtilis solved at a resolution of 2.0 A 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 beta 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 Ndelta, 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 Ni2+ 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.
ER  -

DEMO, Gabriel, Veronika PAPOUŠKOVÁ, Jan KOMÁREK, Pavel KADEŘÁVEK, Olga OTRUSINOVÁ, Pavel SRB, Alzbeta RABATINOVA, Libor KRÁSNÝ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Michaela WIMMEROVÁ. X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase. \textit{Journal of Structural Biology}. San Diego: Academic Press, 2014, roč.~187, č.~2, s.~174-186. ISSN~1047-8477. Dostupné z: https://dx.doi.org/10.1016/j.jsb.2014.06.001.

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