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Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution
1Laboratoire de Biologie Physicochimique-CNRS U.A. 1131, Université Paris-Sud, Orsay, France.
Journal of Molecular Biology
|May 5, 1991
Summary
Bacillus amyloliquefaciens ribonuclease (Barnase) crystal structure reveals d(GpC) binding outside the active site. This non-productive binding may indicate a product site for Barnase after hydrolysis.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Barnase is a ribonuclease secreted by Bacillus amyloliquefaciens.
- Understanding enzyme-inhibitor interactions is crucial for drug design and enzyme mechanism studies.
Purpose of the Study:
- To determine the crystal structure of Barnase co-crystallized with the deoxy-dinucleotide d(GpC).
- To elucidate the binding mode of d(GpC) to Barnase and compare it with other nucleotide-binding interactions.
Main Methods:
- Co-crystallization of Barnase with d(GpC).
- X-ray crystallography and molecular replacement for structure determination.
- Refinement of the crystal structure to 1.9 A resolution.
Main Results:
- The crystal structure of Barnase complexed with d(GpC) was determined with a crystallographic R factor of 22%.
- The protein moiety showed minor differences compared to free Barnase (RMS C alpha movement of 0.45 A).
- The dinucleotide d(GpC) adopted a folded conformation, binding outside the active site through stacking interactions with His102 and hydrogen bonding to the 5' hydroxyl.
Conclusions:
- The observed binding mode of d(GpC) to Barnase is non-productive for substrate hydrolysis.
- This interaction may represent a binding site for the nucleotide product on the 3' side of the cleaved bond.
- The study provides insights into the structural basis of Barnase-nucleotide interactions, distinct from other microbial nucleases.