6QNZ

Crystal structure of the site-specific DNA nickase N.BspD6I E418A Mutant

Summary for 6QNZ

• Entry DOI: 10.2210/pdb6qnz/pdb
• Descriptor: Heterodimeric restriction endonuclease R.BspD6I large subunit, GLYCEROL, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: nickase, endonuclease, nt.bspd6i, nicking, dna, hydrolase
• Biological source: Bacillus sp. D6
• Total number of polymer chains: 2
• Total formula weight: 142289.34

Authors

Artyukh, R.I.,Kachalova, G.S.,Yunusova, A.K.,Gabdulkhakov, A.G.,Fatkhullin, B.F.,Atanasov, B.P.,Perevyazova, T.A.,Popov, A.N.,Zheleznaya, L.A. (deposition date: 2019-02-12, release date: 2020-03-04, Last modification date: 2024-01-24)

Primary citation

Artyukh, R.I.,Kachalova, G.S.,Yunusova, A.K.,Fatkhullin, B.F.,Atanasov, B.P.,Perevyazova, T.A.,Popov, A.N.,Gabdulkhakov, A.G.,Zheleznaya, L.A.
The key role of E418 carboxyl group in the formation of Nt.BspD6I nickase active site: Structural and functional properties of Nt.BspD6I E418A mutant.
J.Struct.Biol., 210:107508-107508, 2020

PubMed Abstract: The mutated nickase Nt.BspD6I E418A has been obtained by site-directed mutagenesis. The purified protein has been crystallized, and its spatial structure has been determined at 2.45 Å resolution. An analysis of the crystal structures of the wild-type and mutated nickase have shown that the elimination of a carboxyl group due to the E418A mutation initiates marked conformational changes in both the N-terminal recognition domain and the C-terminal catalytic domain of nickase and insignificantly affects its linker domain. This is supported by changes in the functional properties of mutated nickase: an increase in the oligomerization capacity in the presence of a substrate, a reduction in the capacity to bind a substrate, and complete loss of catalytic activity.

PubMed: 32298813
DOI: 10.1016/j.jsb.2020.107508

Experimental method

X-RAY DIFFRACTION (2.45 Å)