Neutron and X-ray crystallographic analysis of the human -thrombin-bivalirubin complex at pD 5.0; Protonation states and hydration structure of the enzyme-product complex

Yamada, Taro*; Kurihara, Kazuo; Onishi, Yuki*; Tamada, Taro; Tomoyori, Katsuaki; Masumi, Kenji*; Tanaka, Ichiro*; Kuroki, Ryota; Niimura, Nobuo*

Biochimica et Biophysica Acta; Proteins and Proteomics, 1834(8), p.1532 - 1538, 2013/08

https://doi.org/10.1016/j.bbapap.2013.05.014

The protonation states and hydration structures of the -thrombin-bivalirubin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8 , respectively. The atomic distances were estimated by carrying out X-ray crystallographic analysis at 1.25 resolution. The complex represents a model of the enzyme-product (EP) complex of -thrombin. The neutron scattering length maps around the active site suggest that the side chain of H57/H was deuterated. The joint XN refinement showed that occupancies for D1 and D2 of H57/H were 1.0 and 0.7, respectively. However, no significant neutron scattering length density was observed around the hydroxyl oxygen O of S195/H, which was close to the carboxylic carbon atom of dFPR-COOH. These observations suggest that the O atom of S195/H is deprotonated and maintains its nucleophilicity in the EP complex. In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented.