6QNZ image
Deposition Date 2019-02-12
Release Date 2020-03-04
Last Version Date 2024-01-24
Entry Detail
PDB ID:
6QNZ
Keywords:
Title:
Crystal structure of the site-specific DNA nickase N.BspD6I E418A Mutant
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.45 Å
R-Value Free:
0.24
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Heterodimeric restriction endonuclease R.BspD6I large subunit
Gene (Uniprot):bspD6R1
Mutagens:E418A
Chain IDs:A, B
Chain Length:604
Number of Molecules:2
Biological Source:Bacillus sp. D6
Primary Citation
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)
PMID: 32298813 DOI: 10.1016/j.jsb.2020.107508

Abstact

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.

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Primary Citation of related structures