6JG8

Crystal structure of AimR in complex with DNA

• PDB DOI:  https://doi.org/10.2210/pdb6JG8/pdb
• NAKB: 6JG8

• Classification: PEPTIDE BINDING PROTEIN/DNA
• Organism(s): Spbetavirus SPbeta
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-13 Released: 2019-07-03 
• Deposition Author(s): Guan, Z.Y., Pei, K., Zou, T.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.222 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Literature

Structural insights into DNA recognition by AimR of the arbitrium communication system in the SPbeta phage.

Guan, Z.Y., Pei, K., Wang, J., Cui, Y.Q., Zhu, X., Su, X., Zhou, Y.B., Zhang, D.L., Tang, C., Yin, P., Liu, Z., Zou, T.T.

(2019) Cell Discov 5: 29-29

• PubMed: 31149347 
• DOI: https://doi.org/10.1038/s41421-019-0101-2
• Primary Citation of Related Structures:  
  6JG5, 6JG8, 6JG9


• PubMed Abstract: 
  

A newly identified arbitrium communication system regulates the lysis-to-lysogeny decision in a Bacillus bacteriophage. This system contains an arbitrium hexapeptide as a signal, the cellular receptor AimR, and the lysogenic negative regulator AimX. AimR specifically targets the downstream DNA to activate aimX gene expression. The arbitrium peptide binds to AimR, inhibiting its DNA-binding to promote phage lysogeny. Recently, we and other groups have elucidated how arbitrium peptide sensed by AimR. However, the molecular mechanisms of DNA recognition by AimR and the regulation of its DNA-binding activity by the peptide remain largely unknown. Here, we report the crystal structure of the AimR-DNA complex at 2.1 Å resolution. The N-terminal HTH motif recognizes the palindromic DNA sequence, buttressed by interactions between positively charged residues and the DNA phosphate groups. The DNA-bound AimR assembles a more closed dimer than the peptide-bound form. Single-molecule FRET and crosslinking assays revealed that the AimR protein samples both open and closed conformations in solution. Arbitrium peptide binding induces a closed-to-open conformational change of AimR, eliminating DNA targeting. Our structural and functional analysis provides new insights into the DNA recognition mechanism of AimR and its regulation by the arbitrium peptide in the context of phage lysis-lysogeny decisions.

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Organizational Affiliation: 

3College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 112.21 kDa 
• Atom Count: 7,913 
• Modelled Residue Count: 839 
• Deposited Residue Count: 852 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AimR transcriptional regulator	A, B	395	Spbetavirus SPbeta	Mutation(s): 0  Gene Names: aimR, yopK
UniProt
Find proteins for O64094 (Bacillus phage SPbeta) Explore O64094  Go to UniProtKB:  O64094

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	C	31	Spbetavirus SPbeta

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	D	31	Spbetavirus SPbeta

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.222 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.007	α = 90
b = 98.007	β = 90
c = 159.995	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Guan, Z.Y., Pei, K., Zou, T.T.

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release