The catalytic site of serine proteinases as a specific binding cavity for xenon

Abstract

Background: Under moderate pressure, xenon can bind to proteins and form weak but specific interactions. Such protein-xenon complexes can be used as isomorphous derivatives for phase determination in X-ray crystallography.

Results: Investigation of the serine proteinase class of enzymes shows that the catalytic triad, the common hydrolytic motif of these enzymes, is a specific binding site for one xenon atom and shows high occupancy at pressures below 12 bar. Complexes of xenon with two different serine proteinases, elastase and collagenase, were analyzed and refined to 2.2 A and 2.5 A resolution, respectively. In both cases, a single xenon atom with a low temperature factor is located in the active site at identical positions. Weak interactions exist with several side chains of conserved amino acids at the active site. Xenon binding does not induce any major changes in the protein structure and, as a consequence, crystals of the xenon complexes are highly isomorphous with the native protein structures. Xenon is also found to bind to the active site of subtilisin Carlsberg, a bacterial serine proteinase, that also has a catalytic triad motif.

Conclusions: As the region around the active site shows conserved structural homology in all serine proteinases, it is anticipated that xenon binding will prove to be a general feature of this class of proteins.