Atomic resolution studies of S1 nuclease complexes reveal
details of RNA interaction with the enzyme despite multiple
lattice-translocation defects

J 2022

Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects

ADAMKOVA, Kristyna, Tomas KOVAL, Lars H OSTERGAARD, Jarmila DUSKOVA, Martin MALY et. al.

Základní údaje

Originální název

Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects

Autoři

ADAMKOVA, Kristyna, Tomas KOVAL, Lars H OSTERGAARD, Jarmila DUSKOVA, Martin MALY, Leona SVECOVA, Tereza SKALOVA, Petr KOLENKO a Jan DOHNALEK

Vydání

Acta Crystallographica Section D: Structural Biology, Chester, International Union of Crystallography, 2022, 2059-7983

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.200

Kód RIV

RIV/00216224:14740/22:00128763

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1107/S2059798322008397

UT WoS

000865745200002

Klíčová slova anglicky

S1 nuclease; Aspergillus oryzae; lattice-translocation defects; nucleotides; nucleosides; complexes

Štítky

ne MU, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 2. 2023 15:11, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

S1 nuclease from Aspergillus oryzae is a single-strand-specific nuclease from the S1/P1 family that is utilized in biochemistry and biotechnology. S1 nuclease is active on both RNA and DNA but with differing catalytic efficiencies. This study clarifies its catalytic properties using a thorough comparison of differences in the binding of RNA and DNA in the active site of S1 nuclease based on X-ray structures, including two newly solved complexes of S1 nuclease with the products of RNA cleavage at atomic resolution. Conclusions derived from this comparison are valid for the whole S1/P1 nuclease family. For proper model building and refinement, multiple lattice-translocation defects present in the measured diffraction data needed to be solved. Two different approaches were tested and compared. Correction of the measured intensities proved to be superior to the use of the dislocation model of asymmetric units with partial occupancy of individual chains. As the crystals suffered from multiple lattice translocations, equations for their correction were derived de novo. The presented approach to the correction of multiple lattice-translocation defects may help to solve similar problems in the field of protein X-ray crystallography.

Návaznosti

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

ADAMKOVA, Kristyna, Tomas KOVAL, Lars H OSTERGAARD, Jarmila DUSKOVA, Martin MALY, Leona SVECOVA, Tereza SKALOVA, Petr KOLENKO a Jan DOHNALEK. Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2022, roč. 78, OCT, s. 1194-1209. ISSN 2059-7983. Dostupné z: https://dx.doi.org/10.1107/S2059798322008397.

@article{2262420,
   author = {Adamkova, Kristyna and Koval, Tomas and Ostergaard, Lars H and Duskova, Jarmila and Maly, Martin and Svecova, Leona and Skalova, Tereza and Kolenko, Petr and Dohnalek, Jan},
   article_location = {Chester},
   article_number = {OCT},
   doi = {http://dx.doi.org/10.1107/S2059798322008397},
   keywords = {S1 nuclease; Aspergillus oryzae; lattice-translocation defects; nucleotides; nucleosides; complexes},
   language = {eng},
   issn = {2059-7983},
   journal = {Acta Crystallographica Section D: Structural Biology},
   title = {Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects},
   url = {https://scripts.iucr.org/cgi-bin/paper?S2059798322008397},
   volume = {78},
   year = {2022}
}

TY  - JOUR
ID  - 2262420
AU  - Adamkova, Kristyna - Koval, Tomas - Ostergaard, Lars H - Duskova, Jarmila - Maly, Martin - Svecova, Leona - Skalova, Tereza - Kolenko, Petr - Dohnalek, Jan
PY  - 2022
TI  - Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects
JF  - Acta Crystallographica Section D: Structural Biology
VL  - 78
IS  - OCT
SP  - 1194-1209
EP  - 1194-1209
PB  - International Union of Crystallography
SN  - 20597983
KW  - S1 nuclease
KW  - Aspergillus oryzae
KW  - lattice-translocation defects
KW  - nucleotides
KW  - nucleosides
KW  - complexes
UR  - https://scripts.iucr.org/cgi-bin/paper?S2059798322008397
N2  - S1 nuclease from Aspergillus oryzae is a single-strand-specific nuclease from the S1/P1 family that is utilized in biochemistry and biotechnology. S1 nuclease is active on both RNA and DNA but with differing catalytic efficiencies. This study clarifies its catalytic properties using a thorough comparison of differences in the binding of RNA and DNA in the active site of S1 nuclease based on X-ray structures, including two newly solved complexes of S1 nuclease with the products of RNA cleavage at atomic resolution. Conclusions derived from this comparison are valid for the whole S1/P1 nuclease family. For proper model building and refinement, multiple lattice-translocation defects present in the measured diffraction data needed to be solved. Two different approaches were tested and compared. Correction of the measured intensities proved to be superior to the use of the dislocation model of asymmetric units with partial occupancy of individual chains. As the crystals suffered from multiple lattice translocations, equations for their correction were derived de novo. The presented approach to the correction of multiple lattice-translocation defects may help to solve similar problems in the field of protein X-ray crystallography.
ER  -

ADAMKOVA, Kristyna, Tomas KOVAL, Lars H OSTERGAARD, Jarmila DUSKOVA, Martin MALY, Leona SVECOVA, Tereza SKALOVA, Petr KOLENKO a Jan DOHNALEK. Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects. \textit{Acta Crystallographica Section D: Structural Biology}. Chester: International Union of Crystallography, 2022, roč.~78, OCT, s.~1194-1209. ISSN~2059-7983. Dostupné z: https://dx.doi.org/10.1107/S2059798322008397.

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