2ZA4

Crystal Structural Analysis of Barnase-barstar Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.199 

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Literature

Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation

Urakubo, Y., Ikura, T., Ito, N.

(2008) Protein Sci. 17: 1055-1065

  • DOI: 10.1110/ps.073322508

  • PubMed Abstract: 

    • The complex of barnase (bn) and barstar (bs), which has been widely studied as a model for quantitative analysis of protein-protein interactions, is significantly destabilized by a single mutation, namely, bs Asp39 --> Ala, which corresponds to a cha ...

    The complex of barnase (bn) and barstar (bs), which has been widely studied as a model for quantitative analysis of protein-protein interactions, is significantly destabilized by a single mutation, namely, bs Asp39 --> Ala, which corresponds to a change of 7.7 kcal x mol(-1) in the free energy of binding. However, there has been no structural information available to explain such a drastic destabilization. In the present study, we determined the structure of the mutant complex at 1.58 A resolution by X-ray crystallography. The complex was similar to the wild-type complex in terms of overall and interface structures; however, the hydrogen bond network mediated by water molecules at the interface was significantly different. Several water molecules filled the cavity created by the mutation and consequently caused rearrangement of the hydrated water molecules at the interface. The water molecules were redistributed into a channel-like structure that penetrated into the complex. Furthermore, molecular dynamics simulations showed that the mutation increased the mobility of water molecules at the interface. Since such a drastic change in hydration was not observed in other mutant complexes of bn and bs, the significant destabilization of the interaction may be due to this channel-like structure of hydrated water molecules.

    Organizational Affiliation: 

    Laboratory of Structural Biology, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease
A, C
110Bacillus amyloliquefaciensMutation(s): 1 
EC: 3.1.27.-
Find proteins for P00648 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P00648
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Barstar
B, D
90Bacillus amyloliquefaciensMutation(s): 3 
Find proteins for P11540 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P11540
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.388α = 90.00
b = 110.255β = 114.97
c = 47.272γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance