3ZFK

N-terminal truncated Nuclease Domain of Colicin E7

Summary for 3ZFK

• Entry DOI: 10.2210/pdb3zfk/pdb
• Descriptor: COLICIN-E7, ZINC ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: hydrolase, artificial metallonuclease, allosteric control
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 2
• Total formula weight: 31814.86

Authors

Toth, E.,Czene, A.,Gyurcsik, B.,Otten, H.,Poulsen, J.-C.N.,Larsen, S.,Christensen, H.E.M.,Nagata, K. (deposition date: 2012-12-11, release date: 2013-12-18, Last modification date: 2023-12-20)

Primary citation

Czene, A.,Toth, E.,Nemeth, E.,Otten, H.,Poulsen, J.N.,Christensen, H.E.M.,Rulisek, L.,Nagata, K.,Larsen, S.,Gyurcsik, B.
A New Insight Into the Zinc-Dependent DNA-Cleavage by the Colicin E7 Nuclease: A Crystallographic and Computational Study.
Metallomics, 6:2090-, 2014

PubMed 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 Zn(2+)-ion is proposed to play a role in the catalytic process. These results suggest that the mechanism of the Zn(2+)-containing HNH nucleases needs to be further studied and discussed.

PubMed: 25179124
DOI: 10.1039/C4MT00195H

Experimental method

X-RAY DIFFRACTION (1.7 Å)