A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study

Anikó Czene; Eszter Tóth; Eszter Németh; Harm Otten; Jens-Christian Navarro Poulsen; Hans Erik Mølager Christensen; Lubomír Rulíšek; Kyosuke Nagata; Sine Larsen; Béla Gyurcsik

doi:10.1039/c4mt00195h

A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study

Anikó Czene, Eszter Tóth, Eszter Németh, Harm Otten, Jens-Christian Navarro Poulsen, Hans Erik Mølager Christensen, Lubomír Rulíšek, Kyosuke Nagata, Sine Larsen^*, Béla Gyurcsik

^*Corresponding author af dette arbejde

Kemisk Institut

5 Citationer (Scopus)

67 Downloads (Pure)

Abstract

The nuclease domain of colicin E7 metallonuclease (NColE7) contains its active centre at the C-terminus. The mutant ΔN4-NColE7-C∗-where the four N-terminal residues including the positively charged K446, R447 and K449 are replaced with eight residues from the GST tag-is catalytically inactive. The crystal structure of this mutant demonstrates that its overall fold is very similar to that of the native NColE7 structure. This implicates the stabilizing effect of the remaining N-terminal sequence on the structure of the C-terminal catalytic site and the essential role of the deleted residues in the mechanism of the catalyzed reaction. Complementary QM/MM calculations on the protein-DNA complexes support the less favourable cleavage by the mutant protein than by NColE7. Furthermore, a water molecule as a possible ligand for the Zn²⁺-ion is proposed to play a role in the catalytic process. These results suggest that the mechanism of the Zn²⁺-containing HNH nucleases needs to be further studied and discussed.

Originalsprog	Engelsk
Tidsskrift	Metallomics
Vol/bind	6
Udgave nummer	11
Sider (fra-til)	2090-2099
Antal sider	10
ISSN	1756-5901
DOI	https://doi.org/10.1039/c4mt00195h
Status	Udgivet - 2014

Adgang til dokumentet

10.1039/c4mt00195hLicens: CC BY

c4mt00195hForlagets udgivne version, 3,99 MBLicens: CC BY

Citationsformater

@article{73eaf36c4d4941cb82c1a4701c2f1a10,

title = "A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study",

abstract = "The nuclease domain of colicin E7 metallonuclease (NColE7) contains its active centre at the C-terminus. The mutant ΔN4-NColE7-C∗-where the four N-terminal residues including the positively charged K446, R447 and K449 are replaced with eight residues from the GST tag-is catalytically inactive. The crystal structure of this mutant demonstrates that its overall fold is very similar to that of the native NColE7 structure. This implicates the stabilizing effect of the remaining N-terminal sequence on the structure of the C-terminal catalytic site and the essential role of the deleted residues in the mechanism of the catalyzed reaction. Complementary QM/MM calculations on the protein-DNA complexes support the less favourable cleavage by the mutant protein than by NColE7. Furthermore, a water molecule as a possible ligand for the Zn2+-ion is proposed to play a role in the catalytic process. These results suggest that the mechanism of the Zn2+-containing HNH nucleases needs to be further studied and discussed.",

author = "Anik{\'o} Czene and Eszter T{\'o}th and Eszter N{\'e}meth and Harm Otten and Poulsen, {Jens-Christian Navarro} and Christensen, {Hans Erik M{\o}lager} and Lubom{\'i}r Rul{\'i}{\v s}ek and Kyosuke Nagata and Sine Larsen and B{\'e}la Gyurcsik",

year = "2014",

doi = "10.1039/c4mt00195h",

language = "English",

volume = "6",

pages = "2090--2099",

journal = "Metallomics",

issn = "1756-5901",

publisher = "Royal Society of Chemistry",

number = "11",

}

TY - JOUR

T1 - A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease

T2 - a crystallographic and computational study

AU - Czene, Anikó

AU - Tóth, Eszter

AU - Németh, Eszter

AU - Otten, Harm

AU - Poulsen, Jens-Christian Navarro

AU - Christensen, Hans Erik Mølager

AU - Rulíšek, Lubomír

AU - Nagata, Kyosuke

AU - Larsen, Sine

AU - Gyurcsik, Béla

PY - 2014

Y1 - 2014

N2 - The nuclease domain of colicin E7 metallonuclease (NColE7) contains its active centre at the C-terminus. The mutant ΔN4-NColE7-C∗-where the four N-terminal residues including the positively charged K446, R447 and K449 are replaced with eight residues from the GST tag-is catalytically inactive. The crystal structure of this mutant demonstrates that its overall fold is very similar to that of the native NColE7 structure. This implicates the stabilizing effect of the remaining N-terminal sequence on the structure of the C-terminal catalytic site and the essential role of the deleted residues in the mechanism of the catalyzed reaction. Complementary QM/MM calculations on the protein-DNA complexes support the less favourable cleavage by the mutant protein than by NColE7. Furthermore, a water molecule as a possible ligand for the Zn2+-ion is proposed to play a role in the catalytic process. These results suggest that the mechanism of the Zn2+-containing HNH nucleases needs to be further studied and discussed.

AB - The nuclease domain of colicin E7 metallonuclease (NColE7) contains its active centre at the C-terminus. The mutant ΔN4-NColE7-C∗-where the four N-terminal residues including the positively charged K446, R447 and K449 are replaced with eight residues from the GST tag-is catalytically inactive. The crystal structure of this mutant demonstrates that its overall fold is very similar to that of the native NColE7 structure. This implicates the stabilizing effect of the remaining N-terminal sequence on the structure of the C-terminal catalytic site and the essential role of the deleted residues in the mechanism of the catalyzed reaction. Complementary QM/MM calculations on the protein-DNA complexes support the less favourable cleavage by the mutant protein than by NColE7. Furthermore, a water molecule as a possible ligand for the Zn2+-ion is proposed to play a role in the catalytic process. These results suggest that the mechanism of the Zn2+-containing HNH nucleases needs to be further studied and discussed.

U2 - 10.1039/c4mt00195h

DO - 10.1039/c4mt00195h

M3 - Journal article

C2 - 25179124

AN - SCOPUS:84908143969

SN - 1756-5901

VL - 6

SP - 2090

EP - 2099

JO - Metallomics

JF - Metallomics

IS - 11

ER -

A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study

Abstract

Adgang til dokumentet

Fingeraftryk

Citationsformater