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.

Basic information

Original name

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

Authors

DEMO, Gabriel (703 Slovakia, belonging to the institution), Veronika PAPOUŠKOVÁ (203 Czech Republic, belonging to the institution), Jan KOMÁREK (203 Czech Republic, belonging to the institution), Pavel KADEŘÁVEK (203 Czech Republic, belonging to the institution), Olga OTRUSINOVÁ (203 Czech Republic, belonging to the institution), Pavel SRB (203 Czech Republic, belonging to the institution), Alzbeta RABATINOVA (703 Slovakia), Libor KRÁSNÝ (203 Czech Republic), Lukáš ŽÍDEK (203 Czech Republic, belonging to the institution), Vladimír SKLENÁŘ (203 Czech Republic, belonging to the institution) and Michaela WIMMEROVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.231

RIV identification code

RIV/00216224:14740/14:00073722

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000340217300008

Keywords in English

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

Abstract

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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

EE2.3.30.0009, research and development project

Name: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GA13-16842S, research and development project

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

Investor: Czech Science Foundation

Citovat

DEMO, Gabriel, Veronika PAPOUŠKOVÁ, Jan KOMÁREK, Pavel KADEŘÁVEK, Olga OTRUSINOVÁ, Pavel SRB, Alzbeta RABATINOVA, Libor KRÁSNÝ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ and 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, vol. 187, No 2, p. 174-186. ISSN 1047-8477. Available from: 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 and 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, vol.~187, No~2, p.~174-186. ISSN~1047-8477. Available from: https://dx.doi.org/10.1016/j.jsb.2014.06.001.

Detailed Information on Publication Record