6QNZ | pdb_00006qnz

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

• PDB DOI: https://doi.org/10.2210/pdb6QNZ/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. D6
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-02-12 Released: 2020-03-04 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

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.

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.

(2020) J Struct Biol 210: 107508-107508

• PubMed: 32298813 
• DOI: https://doi.org/10.1016/j.jsb.2020.107508
• Primary Citation Related Structures: 
  6QNZ


• 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.

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Organizational Affiliation: 
• Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia. Electronic address: [e-mail].
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
European Synchrotron Radiation Facility, Grenoble 38000, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 142.29 kDa 
• Atom Count: 9,515 
• Modeled Residue Count: 1,142 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterodimeric restriction endonuclease R.BspD6I large subunit	A, B	604	Bacillus sp. D6	Mutation(s): 1  Gene Names: bspD6R1
UniProt
Find proteins for A3FEV7 (Bacillus sp. D6) Explore A3FEV7  Go to UniProtKB:  A3FEV7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.43	α = 90
b = 92.25	β = 105.61
c = 113.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-04-29
  Changes: Database references
• Version 1.2: 2020-05-20
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description