Structural characteristics of the active site of -Lactamase TOHO-1 determined by combined high-resolution neutron and X-ray crystallography

Kurihara, Kazuo; Sunami, Tomoko; Yamada, Mitsugu; Nitanai, Yasushi*; Okazaki, Nobuo; Adachi, Motoyasu; Tamada, Taro; Shimamura, Tatsuro*; Miyano, Masashi*; Ishii, Yoshikazu*; Kuroki, Ryota

To help resolve questions regarding the catalytic activity of -lactamase, the crystal structure of an unliganded form of the -lactamase Toho-1 with double mutation R274N/R276N (Toho-1/NN) has been determined by the use of high-resolution neutron and X-ray diffraction data. A large single crystal of Toho-1/NN with a dimension of 2.6 2.5 1.3 mm was used to collect 100 K neutron diffraction data to 1.5 resolution and X-ray diffraction data to 1.4 resolution. The structural model of Toho-1/NN was refined to an R-factor of 19.7% using a program PHENIX. The structure showed that Glu166, a catalytic residue of Toho-1, was protonated even at pH 7 nonetheless for the close location to the positively charged side chain amino group (-NH3) of Lys73. It is also found that there is a hydration water network bridging between the protonated Glu166 and the oxyanion hole comprising two main chain nitrogen atoms of Ser70 and Ser237. The neutron structure analysis also revealed the clear configuration of the proposed catalytic water molecule bridging Glu166 and Ser70. These observations are important to understand the catalytic action of -lactamase Toho-1.